de-sweep-synthesis
October 20, 2020
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE,
cache = TRUE
)# my packages
library(tidyverse)
library(readr)
library(vroom)
library(tibble)plot.volcano <- function(overlap){
my.colors = c("#d95f02","#e6ab02","#a6cee3","#7570b3","#66a61e")
df = overlap %>%
# add significance and logFC criteria for plotting
dplyr::mutate(Significance = factor(case_when(
(FDR < 0.05) & (abs(logFC) > 1) & (sweep_gene == "yes") ~ "logFC>1, FDR<0.05, & Sweep Candidate",
(FDR < 0.05) & (abs(logFC) > 1) ~ "logFC>1 & FDR<0.05",
(FDR > 0.05) & (abs(logFC) > 1) ~ "logFC>1 only",
(FDR < 0.05) & (abs(logFC) < 1) ~ "FDR<0.05 only",
(FDR > 0.05) & (abs(logFC) < 1) ~ "NS"),
levels = c("NS",
"FDR<0.05 only",
"logFC>1 only",
"logFC>1 & FDR<0.05",
"logFC>1, FDR<0.05, & Sweep Candidate")))
# now ggplot
ggplot(df, aes(x=logFC, y=-log10(FDR), color=Significance, alpha = 0.7)) +
geom_point(data = subset(df, is.na(sweep_gene)==TRUE)) +
geom_point(data = subset(df, is.na(sweep_gene)==FALSE)) +
scale_color_manual(values=my.colors) +
scale_fill_manual(values=my.colors) +
theme_light()
}
kable.overlap <- function(overlap){
knitr::kable(overlap %>%
# filter only sweep genes, significant, logFC>1
filter(FDR < 0.05,
abs(logFC) > 1,
sweep_gene == "yes") %>%
# select columns
dplyr::select(gene,logFC,FDR,`gene name`,`gene description`)) %>%
kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
}# selective sweep analysis
domGene <- readxl::read_excel("../raw_data/DomGeneFinalSelections.xlsx")
# DE results
DE.root <- read_tsv("../deliverables/DE-root.tsv")
DE.shoot <- read_tsv("../deliverables/DE-shoot.tsv")
DE.node <- read_tsv("../deliverables/DE-node.tsv")
DE.leaf <- read_tsv("../deliverables/DE-leaf.tsv")
DE.meristem <- read_tsv("../deliverables/DE-meristem.tsv")
DE.earlyBudding <- read_tsv("../deliverables/DE-earlyBudding.tsv")
DE.lateBudding <- read_tsv("../deliverables/DE-lateBudding.tsv")
DE.endosperm <- read_tsv("../deliverables/DE-endosperm.tsv")
DE.seedcoat <- read_tsv("../deliverables/DE-seedcoat.tsv")overlap.root <- dplyr::left_join(DE.root,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.shoot <- dplyr::left_join(DE.shoot,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.node <- dplyr::left_join(DE.node,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.leaf <- dplyr::left_join(DE.leaf,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.meristem <- dplyr::left_join(DE.meristem,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.earlyBudding <- dplyr::left_join(DE.earlyBudding,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.endosperm <- dplyr::left_join(DE.endosperm,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.lateBudding <- dplyr::left_join(DE.lateBudding,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
overlap.seedcoat <- dplyr::left_join(DE.seedcoat,
domGene %>% dplyr::rename(gene=`gene name1`) %>% dplyr::mutate(sweep_gene="yes"),
by="gene")
# write files
write_tsv(overlap.root, path="../deliverables/sweep-DE-overlap.root.tsv")
write_tsv(overlap.shoot, path="../deliverables/sweep-DE-overlap.shoot.tsv")
write_tsv(overlap.node, path="../deliverables/sweep-DE-overlap.node.tsv")
write_tsv(overlap.leaf, path="../deliverables/sweep-DE-overlap.leaf.tsv")
write_tsv(overlap.meristem, path="../deliverables/sweep-DE-overlap.meristem.tsv")
write_tsv(overlap.earlyBudding, path="../deliverables/sweep-DE-overlap.earlyBudding.tsv")
write_tsv(overlap.lateBudding, path="../deliverables/sweep-DE-overlap.lateBudding.tsv")
write_tsv(overlap.endosperm, path="../deliverables/sweep-DE-overlap.endosperm.tsv")
write_tsv(overlap.seedcoat, path="../deliverables/sweep-DE-overlap.shoot.tsv")1 Tissues
1.1 Root
plot.volcano(overlap.root)
kable.overlap(overlap.root)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 9.120223 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 7.498244 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 8.920923 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr09g0381571 | 4.852486 | 0.0000000 | 0 | NAD(P)-binding Rossmann-fold superfamily protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 4.337908 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP+ reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0154341 | 1.466929 | 0.0000000 | ALA-INTERACTING SUBUNIT 5, ALIS5 | ALA-interacting subunit 5 (ALIS5); INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast thylakoid lumen, plasma membrane, membrane; EXPRESSED IN: 12 plant structures; EXPRESSED DURING: L mature pollen stage, M germinated pollen stage, 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF284, transmembrane eukaryotic (InterPro:IPR005045); BEST Arabidopsis thaliana protein match is: LEM3 (ligand-effect modulator 3) family protein / CDC50 family protein (TAIR:AT1G16360.1) |
| HanXRQr2_Chr07g0311551 | 10.892605 | 0.0000000 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr05g0227611 | 6.293759 | 0.0000002 | ATSWEET10, SWEET10 | Encodes a member of the SWEET sucrose efflux transporter family proteins. |
| HanXRQr2_Chr05g0230361 | 4.953622 | 0.0000002 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr16g0749261 | 8.242572 | 0.0000003 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr05g0216981 | -2.695709 | 0.0000014 | 0 | Pyruvate kinase family protein;(source:Araport11) |
| HanXRQr2_Chr12g0550641 | -2.300580 | 0.0000037 | LOB DOMAIN-CONTAINING PROTEIN 41 (LBD41) | LOB domain-containing protein 41;(source:Araport11) |
| HanXRQr2_Chr03g0127971 | -6.620700 | 0.0000044 | (BHLH014); (BHLH14) | bHLH14 interacts with JAZ proteins, and functions redundantly with bHLH3, bHLH13 and bHLH17 to negatively regulate jasmonate responses. |
| HanXRQr2_Chr07g0284351 | 5.166246 | 0.0000164 | ANAC043, ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 43, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1, NST1 | NAC transcription factor NST1. NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls and siliques. An NST1 promoter fusion was detected in various tissues in which lignified secondary walls develop. Both MYC2 and MYC4 bind to the NST1 promoter and appear to regulate its expression in response to blue light. |
| HanXRQr2_Chr07g0311941 | 6.575199 | 0.0000191 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 6.575199 | 0.0000191 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr13g0577061 | 3.452013 | 0.0000363 | BRASSINOSTEROID-RESPONSIVE RING-H2 (BRH1) | Encodes a novel ring finger protein and forms an N-terminal hydrophobic domain and a C-terminal RING-H2 signature. Expression is down regulated by brassinolide. |
| HanXRQr2_Chr07g0292811 | 4.710127 | 0.0000548 | NA | NA |
| HanXRQr2_Chr04g0158921 | 2.522912 | 0.0000609 | BETA-XYLOSIDASE 2 (ATBXL2);BETA-XYLOSIDASE 2 (BXL2) | encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members. |
| HanXRQr2_Chr06g0251521 | -1.144991 | 0.0000620 | ATEBP, EBP, ERF72, ETHYLENE RESPONSE FACTOR 72, ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN, RAP2.3, RELATED TO AP2 3 | Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr06g0261551 | 4.363842 | 0.0001197 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr17g0793231 | 6.227209 | 0.0001837 | (AtCIB22);B22 SUBUNIT OF EUKARYOTIC MITOCHONDRIAL COMPLEX I (CIB22) | Encodes the B22 subunit of eukaryotic mitochondrial Complex I. Mutation in the gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr10g0449721 | 5.464427 | 0.0001888 | (ATU2AF65B); (U2AF65B) | Putative U2A65 splicing factor which functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in shoot apex. Regulates flowering time and displays a redundant role in pollen tube growth together with AtU2AF65a. |
| HanXRQr2_Chr16g0744861 | 1.267004 | 0.0001894 | APRR2, PRR2, PSEUDO-RESPONSE REGULATOR 2 | Encodes pseudo-response regulator 2 (APRR2) that interacts with a calcium sensor (CML9). |
| HanXRQr2_Chr12g0552841 | -1.909993 | 0.0002034 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr13g0593361 | 3.872969 | 0.0002359 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr12g0533611 | -1.052572 | 0.0002799 | 0 | CDK inhibitor P21 binding protein;(source:Araport11) |
| HanXRQr2_Chr04g0181781 | -7.951606 | 0.0008667 | ARABIDOPSIS THALIANA P GLYCOPROTEIN1 (ATPGP1);ATP-BINDING CASSETTE B1 (ABCB1);P-GLYCOPROTEIN 1 (PGP1) | Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR1.Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AT3G28860. PGP1 mediates cellular efflux of IAA and interacts with PIN genes that may confer an accelerated vectoral component to PGP-mediated transport. The non-polar localization of PGP1 at root and shoot apices, where IAA gradient-driven transport is impaired, may be required to confer directionality to auxin transport in those tissues. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0552691 | 2.077689 | 0.0008952 | IRX15-LIKE (IRX15-L) | Encode a DUF579 (domain of unknown function 579) containing protein essential for normal xylan synthesis and deposition in the secondary cell wall. |
| HanXRQr2_Chr11g0485451 | -7.033963 | 0.0010746 | UDP-GLUCOSYL TRANSFERASE 85A3 (AtUGT85A3);UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) | Encodes a putative UDP-glucosyl transferase. At1g22380 was initially identified as encoding the protein AAF87154, which has been classified as a bHLH protein (AtbHLH152). Subsequently it has been found that the AAF87154 protein appears to be encoded by the AT1G23970 genomic locus. |
| HanXRQr2_Chr06g0246761 | -1.078323 | 0.0011924 | G-BOX BINDING FACTOR 3, GBF3 | encodes a bZIP G-box binding protein whose expression is induced by ABA. It has been shown to bind to Adh that contains the G-box and is induced by cold and water deprivation. GBF3 has been shown to be expressed mostly in the root and dark-grown leaves. GBF3 can act as homodimers and as heterodimers with GFB1, GBF2 and GBF4. In addition, GBF3¡¯s DNA binding activity is enhanced by GIP1, GPRI1 and GPRI2. |
| HanXRQr2_Chr03g0127771 | -3.736632 | 0.0012598 | DMR6-LIKE OXYGENASE 2 (DLO2) | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein;(source:Araport11) |
| HanXRQr2_Chr09g0379931 | 1.463455 | 0.0013136 | (PLA IIB);PATATIN-LIKE PROTEIN 6 (PLP6) | PATATIN-like protein 6;(source:Araport11) |
| HanXRQr2_Chr13g0600371 | 2.653883 | 0.0013813 | PHOSPHORIBULOKINASE (PRK) | phosphoribulokinase;(source:Araport11) |
| HanXRQr2_Chr04g0160511 | 3.026744 | 0.0013942 | NA | Thiamine pyrophosphate dependent pyruvate decarboxylase family protein |
| HanXRQr2_Chr11g0475771 | -2.449115 | 0.0023080 | LYSM RLK1-INTERACTING KINASE 1 (LIK1) | Encodes LRR-RLK protein that is localized to the plasma membrane and is involved in regulation of plant innate immunity to microbes. LIK1 is phosphorylated by CERK1, a kinase involved in chitin perception. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr02g0049271 | -2.635438 | 0.0023396 | CER3, ECERIFERUM 3, FACELESS POLLEN 1, FLP1, WAX2, YRE | encodes a transmembrane protein with similarity to the sterol desaturase family at the N-terminus and to the short-chain dehydrogenase/reductase family at the C-terminus. Mutant analyses indicate this protein is involved in cuticle membrane and wax biosynthesis. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr10g0455621 | 2.670265 | 0.0024012 | LUPEOL SYNTHASE 2 (ATLUP2);LUPEOL SYNTHASE 2 (LUP2) | Encodes a multifunctional 2-3-oxidosqualene (OS)-triterpene cyclase that can cyclize OS into lupeol, alpha- and beta-amyrin. |
| HanXRQr2_Chr02g0066401 | 1.518531 | 0.0032569 | OBF4, OCS ELEMENT BINDING FACTOR 4, TGA4, TGACG MOTIF-BINDING FACTOR 4 | Encodes a member of basic leucine zipper transcription gene family. Nomenclature according to Xiang, et al. (1997). |
| HanXRQr2_Chr15g0689331 | 5.270118 | 0.0032691 | 0 | ATP synthase subunit B;(source:Araport11) |
| HanXRQr2_Chr11g0509401 | -8.624812 | 0.0033596 | ACH1, ATNRT2.1, ATNRT2:1, LATERAL ROOT INITIATION 1, LIN1, NITRATE TRANSPORTER 2, NITRATE TRANSPORTER 2.1, NITRATE TRANSPORTER 2:1, NRT2, NRT2.1, NRT2:1, NRT2;1AT | High-affinity nitrate transporter. Up-regulated by nitrate. Functions as a repressor of lateral root initiation independently of nitrate uptake. |
| HanXRQr2_Chr15g0692621 | -2.370961 | 0.0037848 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr08g0348501 | 1.691645 | 0.0042809 | 0 | AGC (cAMP-dependent, cGMP-dependent and protein kinase C) kinase family protein;(source:Araport11) |
| HanXRQr2_Chr14g0644791 | -5.091828 | 0.0044678 | CYSTEINE-RICH RLK (RECEPTOR-LIKE PROTEIN KINASE) 3 (CRK3) | Encodes a cysteine-rich receptor-like protein kinase. |
| HanXRQr2_Chr14g0627041 | 1.811299 | 0.0044759 | CYCLIC NUCLEOTIDE-BINDING TRANSPORTER 1 (CNBT1);CYCLIC NUCLEOTIDE GATED CHANNEL 20 (CNGC20);CYCLIC NUCLEOTIDE-GATED CHANNEL 20 (ATCNGC20) | cyclic nucleotide-binding transporter 1, member of a family of cyclic nucleotide gated channels. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0748121 | 1.009551 | 0.0051651 | XYLEM CYSTEINE PEPTIDASE 1 (XCP1) | tracheary element vacuolar protein |
| HanXRQr2_Chr09g0405521 | 6.321227 | 0.0062594 | CLAVATA 1 (CLV1); (ATCLV1);FLOWER DEVELOPMENT 5 (FLO5);FASCIATA 3 (FAS3) | Putative receptor kinase with an extracellular leucine-rich domain. Controls shoot and floral meristem size, and contributes to establish and maintain floral meristem identity. Negatively regulated by KAPP (kinase-associated protein phosphatase). CLV3 peptide binds directly CLV1 ectodomain. |
| HanXRQr2_Chr11g0479151 | 1.177517 | 0.0066912 | FORMIN HOMOLOGY5 (Fh5);FORMIN HOMOLOGY 5 (ATFH5) | Encodes a protein with similarity to formins that is involved in cytokinesis. Loss of function mutations exhibit delayed cellularization during endosperm development. FH5 is expressed in the endosperm and the protein localizes to the cell plate. FH5 was shown to be a maternally expressed imprinted gene. |
| HanXRQr2_Chr04g0145031 | 1.703841 | 0.0069851 | SNF1-RELATED PROTEIN KINASE 3.24 (SnRK3.24);CBL-INTERACTING PROTEIN KINASE 5 (CIPK5) | Encodes CBL-interacting protein kinase 5 (CIPK5). |
| HanXRQr2_Chr04g0149371 | 2.546334 | 0.0070865 | CYTOCHROME P450, FAMILY 71, SUBFAMILY A, POLYPEPTIDE 22 (CYP71A22) | putative cytochrome P450 |
| HanXRQr2_Chr15g0690001 | 1.341981 | 0.0072900 | ARABIDOPSIS THALIANA HOMEOBOX 1 (ATHB1); (HD-ZIP-1);HOMEOBOX 1 (ATHB-1);HOMEOBOX 1 (HB-1);HOMEODOMAIN PROTEIN FROM ARABIDOIPSIS THALIANA 5 (HAT5) | Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf and hypocotyl development. Its promoter is bound by PIF1 which likely regulates its expression. Its translation is regulated by a conserved upstream ORF (CPuORF33). |
| HanXRQr2_Chr16g0763511 | 2.129230 | 0.0074324 | (ATSTE14); (STE14);HOMOLOG OF YEAST STE14 A (ATSTE14A);HOMOLOG OF YEAST STE14 A (STE14A);ARABIDOPSIS THALIANA ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ATICMTA);ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ICMTA);LPHA-CARBOXYL METHYLTRANSFERASE (ATPCM) | Encodes a prenylcysteine alpha-carboxyl methyltransferase involved in methylation of isoprenylated proteins. This protein appears to have lower catalytic activity and a lower transcript expression level than the other ICMT present in Arabidopsis (At5g08335). Analysis of ICMT RNAi lines suggests that this protein may be involved in flower and stem development. |
| HanXRQr2_Chr08g0355391 | 2.312040 | 0.0084205 | DAF-LIKE GENE 2 (DAFL2) | RING/U-box superfamily protein; FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 10 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, C globular stage, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, C3HC4 RING-type (InterPro:IPR018957); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT3G10910.1). |
| HanXRQr2_Chr07g0309641 | -2.894532 | 0.0089212 | AGAMOUS-LIKE 8, AGL8, FRUITFULL, FUL | MADS box gene negatively regulated by APETALA1 |
| HanXRQr2_Chr04g0173701 | 3.371487 | 0.0090180 | SENESCENCE-RELATED GENE 1 (ATSRG1);SENESCENCE-RELATED GENE 1 (SRG1) | Encodes a novel member of the Fe(II)/ascorbate oxidase gene family; senescence-related gene. |
| HanXRQr2_Chr12g0543911 | 1.196026 | 0.0102108 | VENOSA 4 (VEN4) | Protein of unknown function involved in chloroplast development. |
| HanXRQr2_Chr14g0639781 | -1.195143 | 0.0105691 | GLUTAMATE DEHYDROGENASE 3 (GDH3) | GDH3 encodes a member of the glutamate dehydrogenease family. Its expression is upregulated in response to cytokinin and it may play a role in the control of nitrogen metabolism in leaf development. |
| HanXRQr2_Chr11g0476721 | 1.161388 | 0.0118389 | TCP3, TEOSINTE BRANCHED 1, CYCLOIDEA AND PCF TRANSCRIPTION FACTOR 3 | Encodes a member of a recently identified plant transcription factor family that includes Teosinte branched 1, Cycloidea 1, and proliferating cell nuclear antigen (PCNA) factors, PCF1 and 2. Regulated by miR319. Involved in heterochronic regulation of leaf differentiation |
| HanXRQr2_Chr15g0706001 | 1.623488 | 0.0119332 | AGAMOUS-LIKE 22, AGL22, FAQ1, FLOWERING ARABIDOPSIS QTL1, SHORT VEGETATIVE PHASE, SVP | Encodes a nuclear protein that acts as a floral repressor and that functions within the thermosensory pathway. SVP represses FT expression via direct binding to the vCArG III motif in the FT promoter. |
| HanXRQr2_Chr10g0423911 | 2.647811 | 0.0128522 | AUTOINHIBITED CA(2+)-ATPASE, ISOFORM 4 (ACA4) | Encodes a calmodulin-regulated Ca(2+)-ATPase that improves salt tolerance in yeast. Localized to the vacuole. Lesion mimic phenotype when mutation in the gene is combined with a mutation in ACA11. Lesion mimic phenotype of double knockout can be suppressed by nutritional supplements that increase anion levels (e.g. 15 mM Nitrate, Chloride, or Phosphate). |
| HanXRQr2_Chr04g0159101 | -2.082478 | 0.0132579 | 0 | Class-II DAHP synthetase family protein;(source:Araport11) |
| HanXRQr2_Chr09g0380251 | -2.145509 | 0.0146202 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr04g0154021 | 5.697398 | 0.0174676 | RECEPTOR LIKE PROTEIN 34 (AtRLP34);RECEPTOR LIKE PROTEIN 34 (RLP34) | receptor like protein 34;(source:Araport11) |
| HanXRQr2_Chr08g0342321 | -1.757274 | 0.0176694 | MAP KINASE KINASE 9 (MKK9); (ATMKK9) | member of MAP Kinase Kinase family. Autophosphorylates and also phosphorylates MPK3 and MPK6. Independently involved in ethylene and calmalexin biosynthesis. Induces transcription of ACS2, ACS6, ERF1, ERF2, ERF5, ERF6, CYP79B2, CYP79B3, CYP71A13 and PAD3. |
| HanXRQr2_Chr03g0095001 | 1.025963 | 0.0263423 | SMAX1-LIKE 2 (SMXL2) | Encodes a member of an eight-gene family (SMAX1 and SMAX1-like) that has weak similarity to AtHSP101, a ClpB chaperonin required for thermotolerance. |
| HanXRQr2_Chr16g0757041 | 1.362220 | 0.0299076 | ETTIN (ETT);AUXIN RESPONSE TRANSCRIPTION FACTOR 3 (ARF3) | ettin (ett) mutations have pleiotropic effects on Arabidopsis flower development, causing increases in perianth organ number, decreases in stamen number and anther formation, and apical-basal patterning defects in the gynoecium. The ETTIN gene encodes a protein with homology to DNA binding proteins which bind to auxin response elements. ETT transcript is expressed throughout stage 1 floral meristems and subsequently resolves to a complex pattern within petal, stamen and carpel primordia. ETT probably functions to impart regional identity in floral meristems that affects perianth organ number spacing, stamen formation, and regional differentiation in stamens and the gynoecium. During stage 5, ETT expression appears in a ring at the top of the floral meristem before morphological appearance of the gynoecium, consistent with the proposal that ETT is involved in prepatterning apical and basal boundaries in the gynoecium primordium. It is a target of the ta-siRNA tasiR-ARF. ETT is also a target of AP2; integrateing the functions of AGAMOUS and APETALA2 in floral meristem determinacy. Positive regulation of drought stress response genes. |
| HanXRQr2_Chr01g0024991 | 1.398690 | 0.0306886 | ACA1 | Encodes a chloroplast envelope Ca2+-ATPase with an N-terminal autoinhibitor. |
| HanXRQr2_Chr02g0051561 | 1.682146 | 0.0318216 | CAB UNDEREXPRESSED 1 (CUE1);NITROUS OXIDE OVEREXPRESSOR 1 (NOX1);ARABIDOPSIS THALIANA PHOSPHATE/PHOSPHOENOLPYRUVATE TRANSLOCATOR (ARAPPT);PHOSPHOENOLPYRUVATE/PHOSPHATE TRANSLOCATOR (PPT) | Encodes a plastid inner envelope protein PPT (phosphoenolpyruvate/phosphate translocator) that catalyzes the transport of phosphoenolpyruvate and phosphate across the inner envelope membrane of plastids. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr08g0355341 | 5.294460 | 0.0340450 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr02g0047981 | 3.390142 | 0.0373647 | 0 | alpha/beta-Hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr09g0372751 | -2.759142 | 0.0400590 | NA | Glycosyl hydrolase family 10 protein |
| HanXRQr2_Chr01g0025561 | 2.503236 | 0.0413985 | FATTY ACID EXPORT 1, FAX1 | Encodes a chloroplast inner envelope localized member of the Tmemb_14 gene family. FAX1 is involved in fatty acid and lipid homeostasis and likely functions as a fatty acid transporter that exports fatty acids from the plastid. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr14g0626821 | 4.583269 | 0.0456466 | FLOWERING LOCUS T (FT) | FT, together with LFY, promotes flowering and is antagonistic with its homologous gene, TERMINAL FLOWER1 (TFL1). Together with TSF, it plays an antagonistic role to TFL1 in the determination of inflorescence meristem identity. FT is expressed in leaves and is induced by long day treatment. Either the FT mRNA or protein is translocated to the shoot apex where it induces its own expression. Recent data suggests that FT protein acts as a long-range signal. FT is a target of CO and acts upstream of SOC1. |
| HanXRQr2_Chr04g0160171 | 1.805792 | 0.0458120 | XYLOGLUCAN ENDOTRANSGLYCOSYLASE RELATED 2 (XTR2);XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 28 (XTH28); (ATXTH28);ENDOXYLOGLUCAN TRANSFERASE A2 (EXGT-A2) | member of Glycoside Hydrolase Family 16 |
| HanXRQr2_Chr10g0442381 | 2.389616 | 0.0491925 | SERINE HYDROXYMETHYLTRANSFERASE 6 (SHM6) | Encodes a putative serine hydroxymethyltransferase. |
1.2 Shoot
plot.volcano(overlap.shoot)
kable.overlap(overlap.shoot)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 8.017204 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 8.459612 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr05g0216981 | -4.925006 | 0.0000000 | 0 | Pyruvate kinase family protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 6.871105 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr09g0377061 | -2.135207 | 0.0000000 | DICARBOXYLATE TRANSPORT 2.1 (DIT2.1); (DCT) | dicarboxylate transport 2.1;(source:Araport11) |
| HanXRQr2_Chr12g0550641 | -3.441294 | 0.0000000 | LOB DOMAIN-CONTAINING PROTEIN 41 (LBD41) | LOB domain-containing protein 41;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 4.189547 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0311551 | 10.671210 | 0.0000001 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr04g0154341 | 1.341756 | 0.0000001 | ALA-INTERACTING SUBUNIT 5, ALIS5 | ALA-interacting subunit 5 (ALIS5); INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast thylakoid lumen, plasma membrane, membrane; EXPRESSED IN: 12 plant structures; EXPRESSED DURING: L mature pollen stage, M germinated pollen stage, 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF284, transmembrane eukaryotic (InterPro:IPR005045); BEST Arabidopsis thaliana protein match is: LEM3 (ligand-effect modulator 3) family protein / CDC50 family protein (TAIR:AT1G16360.1) |
| HanXRQr2_Chr05g0230361 | 5.221000 | 0.0000002 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr16g0749261 | 8.513733 | 0.0000003 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr13g0600371 | 1.585591 | 0.0000010 | PHOSPHORIBULOKINASE (PRK) | phosphoribulokinase;(source:Araport11) |
| HanXRQr2_Chr12g0551671 | -2.321453 | 0.0000014 | PEROXISOMAL NAD-MALATE DEHYDROGENASE 1 (PMDH1) | encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA. |
| HanXRQr2_Chr05g0227611 | 6.057666 | 0.0000019 | ATSWEET10, SWEET10 | Encodes a member of the SWEET sucrose efflux transporter family proteins. |
| HanXRQr2_Chr10g0449721 | 7.898519 | 0.0000025 | (ATU2AF65B); (U2AF65B) | Putative U2A65 splicing factor which functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in shoot apex. Regulates flowering time and displays a redundant role in pollen tube growth together with AtU2AF65a. |
| HanXRQr2_Chr16g0757701 | 2.099554 | 0.0000038 | INCREASED PETAL GROWTH ANISOTROPY 1, IPGA1 | Microtubule associated protein involved in cortical microtubule organization. |
| HanXRQr2_Chr15g0708701 | -4.540851 | 0.0000044 | NITRATE REDUCTASE 2 (NIA2); (B29); (NIA2-1);ARABIDOPSIS NITRATE REDUCTASE 2 (ATNR2);NITRATE REDUCTASE (NR);NITRATE REDUCTASE 2 (NR2);CHLORATE RESISTANT 3 (CHL3) | Identified as a mutant resistant to chlorate. Encodes nitrate reductase structural gene. Involved in nitrate assimilation. Has nitrate reductase activity. Up-regulated by the fungus P. indica. Binds transcription factor At2g35940. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0159741 | -1.072614 | 0.0000048 | PESCADILLO (PES) | Encodes a nucleolar protein that plays an essential role in cell growth and survival through its regulation of ribosome biogenesis and mitotic progression. |
| HanXRQr2_Chr06g0241411 | -1.152017 | 0.0000077 | SPA1-RELATED 2 (SPA2) | Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA proteins function redundantly in suppressing photomorphogenesis in dark- and light-grown seedlings. SPA2 primarily regulates seedling development in darkness and has little function in light-grown seedlings or adult plants. |
| HanXRQr2_Chr12g0551621 | 1.349687 | 0.0000119 | NA | UDP-Glycosyltransferase superfamily protein |
| HanXRQr2_Chr15g0690001 | 2.353181 | 0.0000158 | ARABIDOPSIS THALIANA HOMEOBOX 1 (ATHB1); (HD-ZIP-1);HOMEOBOX 1 (ATHB-1);HOMEOBOX 1 (HB-1);HOMEODOMAIN PROTEIN FROM ARABIDOIPSIS THALIANA 5 (HAT5) | Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf and hypocotyl development. Its promoter is bound by PIF1 which likely regulates its expression. Its translation is regulated by a conserved upstream ORF (CPuORF33). |
| HanXRQr2_Chr12g0533581 | 2.194232 | 0.0000176 | CHLORORESPIRATORY REDUCTION 23 (CRR23);NADH DEHYDROGENASE-LIKE COMPLEX L (NdhL) | a subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in PSI cyclic electron transport. Located on the thylakoid membrane. Mutant has impaired NAD(P)H dehydrogenase activity. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr06g0261551 | 4.958866 | 0.0000362 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr13g0607011 | 1.526484 | 0.0000991 | HOMEOBOX PROTEIN 2 (ATHB-2);HOMEOBOX PROTEIN 2 (HB-2);ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2 (ATHB2); (HAT4) | Encodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0381571 | 1.819360 | 0.0001172 | 0 | NAD(P)-binding Rossmann-fold superfamily protein;(source:Araport11) |
| HanXRQr2_Chr17g0793231 | 6.947458 | 0.0001499 | (AtCIB22);B22 SUBUNIT OF EUKARYOTIC MITOCHONDRIAL COMPLEX I (CIB22) | Encodes the B22 subunit of eukaryotic mitochondrial Complex I. Mutation in the gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr13g0593361 | 4.204013 | 0.0001646 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr11g0479121 | -2.090833 | 0.0001971 | PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) | Member of GRAS gene family. Semi-dominant mutant has a reduced response to far-red light and appears to act early in the phytochrome A signaling pathway. |
| HanXRQr2_Chr14g0639781 | -1.811133 | 0.0002057 | GLUTAMATE DEHYDROGENASE 3 (GDH3) | GDH3 encodes a member of the glutamate dehydrogenease family. Its expression is upregulated in response to cytokinin and it may play a role in the control of nitrogen metabolism in leaf development. |
| HanXRQr2_Chr14g0650761 | -1.020377 | 0.0003466 | NA | Ribonuclease III family protein; FUNCTIONS IN: RNA binding, ribonuclease III activity; INVOLVED IN: RNA processing; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribonuclease III (InterPro:IPR000999); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT2G48121.2) |
| HanXRQr2_Chr11g0475771 | -3.162644 | 0.0003972 | LYSM RLK1-INTERACTING KINASE 1 (LIK1) | Encodes LRR-RLK protein that is localized to the plasma membrane and is involved in regulation of plant innate immunity to microbes. LIK1 is phosphorylated by CERK1, a kinase involved in chitin perception. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0744931 | 2.654757 | 0.0004248 | ARABIDOPSIS THALIANA TONOPLAST INTRINSIC PROTEIN 2;3 (ATTIP2;3);TONOPLAST INTRINSIC PROTEIN 2;3 (TIP2;3);DELTA-TONOPLAST INTRINSIC PROTEIN 3 (DELTA-TIP3) | Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3). |
| HanXRQr2_Chr16g0749351 | 1.213972 | 0.0004267 | PAP3, PHOTOCURRENT 1, PHYTOCHROME INTERACTING FACTOR 3, PHYTOCHROME-ASSOCIATED PROTEIN 3, PIF3, POC1 | Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes. |
| HanXRQr2_Chr07g0311941 | 3.085246 | 0.0004328 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 3.085246 | 0.0004328 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr09g0409291 | 3.622718 | 0.0005216 | ABA-IMPORTING TRANSPORTER 1, AIT1, ATNPF4.6, ATNRT1:2, NITRATE TRANSPORTER 1:2, NPF4.6, NRT1.2, NRT1/ PTR FAMILY 4.6, NRT1:2, NTL1 | Encodes an inducible component of low-affinity nitrate uptake. mRNA found primarily in root hairs and the epidermis of roots. It also acts as an ABA importer at the site of ABA biosynthesis and is important for the regulation of stomatal aperture in inflorescence stems. |
| HanXRQr2_Chr06g0258881 | 1.027769 | 0.0006612 | DISPROPORTIONATING ENZYME 2 (DPE2) | Encodes a cytosolic protein with transglucosidase and amylomaltase activity. It is an essential component of the pathway from starch to sucrose and cellular metabolism in leaves at night. The protein binds to heteroglycans and utilizes glucose, mannose and xylose as acceptors. Fucose and galactose can also act as acceptors but less efficiently than the previous three. It was also was also recently reported to act on maltodextrins. On the other hand, arabinose and fructose were not efficiently used. Its role probably includes metabolizing maltose exported from the chloroplast. Studies using maltose extracted from the double mutant be2-1 be3-2 showed that this enzyme is preferentially active of β-maltose. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr02g0049271 | -2.725869 | 0.0009788 | CER3, ECERIFERUM 3, FACELESS POLLEN 1, FLP1, WAX2, YRE | encodes a transmembrane protein with similarity to the sterol desaturase family at the N-terminus and to the short-chain dehydrogenase/reductase family at the C-terminus. Mutant analyses indicate this protein is involved in cuticle membrane and wax biosynthesis. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr11g0476721 | 1.440704 | 0.0013259 | TCP3, TEOSINTE BRANCHED 1, CYCLOIDEA AND PCF TRANSCRIPTION FACTOR 3 | Encodes a member of a recently identified plant transcription factor family that includes Teosinte branched 1, Cycloidea 1, and proliferating cell nuclear antigen (PCNA) factors, PCF1 and 2. Regulated by miR319. Involved in heterochronic regulation of leaf differentiation |
| HanXRQr2_Chr03g0127771 | -4.395035 | 0.0013905 | DMR6-LIKE OXYGENASE 2 (DLO2) | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein;(source:Araport11) |
| HanXRQr2_Chr04g0181781 | -9.584919 | 0.0014118 | ARABIDOPSIS THALIANA P GLYCOPROTEIN1 (ATPGP1);ATP-BINDING CASSETTE B1 (ABCB1);P-GLYCOPROTEIN 1 (PGP1) | Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR1.Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AT3G28860. PGP1 mediates cellular efflux of IAA and interacts with PIN genes that may confer an accelerated vectoral component to PGP-mediated transport. The non-polar localization of PGP1 at root and shoot apices, where IAA gradient-driven transport is impaired, may be required to confer directionality to auxin transport in those tissues. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr14g0657451 | -2.595546 | 0.0016753 | FAD2-1!!! | Major enzyme responsible for the synthesis of 18:2 fatty acids in the endoplasmic reticulum. Contains His-rich motifs, which contribute to the interaction with the electron donor cytochrome b5. Mutations in this gene suppress the low temperature-induced phenotype of Arabidopsis tocopherol-deficient mutant vte2. |
| HanXRQr2_Chr11g0474921 | -3.128654 | 0.0017647 | ARABIDOPSIS THALIANA GIBBERELLIN 2-OXIDASE 1, ATGA2OX1, GA2OX1, GIBBERELLIN 2-OXIDASE 1 | Encodes a gibberellin 2-oxidase that acts on C19 gibberellins. |
| HanXRQr2_Chr04g0160391 | -8.834746 | 0.0018273 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr11g0520671 | -1.295470 | 0.0023333 | E-COAH-2, ECHIA, ENOYL-COA HYDRATASE 2, ENOYL-COA HYDRATASE/ISOMERASE A | enoyl-CoA hydratase/isomerase A (ECHIA); FUNCTIONS IN: catalytic activity; INVOLVED IN: metabolic process; LOCATED IN: peroxisome; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Crotonase, core (InterPro:IPR001753); BEST Arabidopsis thaliana protein match is: enoyl-CoA hydratase/isomerase D (TAIR:AT1G60550.1) |
| HanXRQr2_Chr12g0557131 | -1.064443 | 0.0023529 | K+ UPTAKE PERMEASE 11 (KUP11) | potassium transporter |
| HanXRQr2_Chr09g0380251 | -2.784532 | 0.0031639 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr08g0336081 | 3.198281 | 0.0032397 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr14g0659991 | -1.911546 | 0.0035387 | ANGUSTIFOLIA 3 (AN3);GRF1-INTERACTING FACTOR (GIF);ARABIDOPSIS GRF1-INTERACTING FACTOR 1 (ATGIF1);GRF1-INTERACTING FACTOR 1 (GIF1) | Encodes a protein with similarity to mammalian transcriptional coactivator that is involved in cell proliferation during leaf and flower development. Loss of function mutations have narrow, pointed leaves and narrow floral organs. AN3 interacts with members of the growth regulating factor (GRF) family of transcription factors. |
| HanXRQr2_Chr14g0644791 | -5.799404 | 0.0038359 | CYSTEINE-RICH RLK (RECEPTOR-LIKE PROTEIN KINASE) 3 (CRK3) | Encodes a cysteine-rich receptor-like protein kinase. |
| HanXRQr2_Chr14g0626961 | -3.269672 | 0.0039832 | 0 | Ankyrin-repeat containing protein;(source:Araport11) |
| HanXRQr2_Chr10g0444291 | 1.058809 | 0.0039834 | DCT, DICARBOXYLATE TRANSPORT 2.1, DIT2.1 | dicarboxylate transport 2.1 |
| HanXRQr2_Chr16g0735881 | -1.015188 | 0.0041279 | NA | tRNA-processing ribonuclease BN;(source:Araport11) |
| HanXRQr2_Chr17g0781641 | -1.475022 | 0.0041957 | AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 21 (AHL21);GIANT KILLER (GIK) | Direct target of AGAMOUS. Regulates patterning and differentiation of reproductive organs. |
| HanXRQr2_Chr03g0114791 | -1.050017 | 0.0042733 | EMBRYO DEFECTIVE 3120 (EMB3120) | hypothetical protein;(source:Araport11) |
| HanXRQr2_Chr14g0657161 | 2.264293 | 0.0048779 | ABA-RESPONSIVE KINASE SUBSTRATE 3 (AKS3);FLOWERING BHLH 4 (FBH4) | basic helix-loop-helix (bHLH) DNA-binding superfamily protein;(source:Araport11) |
| HanXRQr2_Chr04g0145031 | 1.784344 | 0.0049065 | SNF1-RELATED PROTEIN KINASE 3.24 (SnRK3.24);CBL-INTERACTING PROTEIN KINASE 5 (CIPK5) | Encodes CBL-interacting protein kinase 5 (CIPK5). |
| HanXRQr2_Chr02g0066401 | 1.456223 | 0.0050781 | OBF4, OCS ELEMENT BINDING FACTOR 4, TGA4, TGACG MOTIF-BINDING FACTOR 4 | Encodes a member of basic leucine zipper transcription gene family. Nomenclature according to Xiang, et al. (1997). |
| HanXRQr2_Chr01g0024971 | 2.263886 | 0.0052541 | ATCKX1, CKX1, CYTOKININ OXIDASE/DEHYDROGENASE 1 | It encodes a protein whose sequence is similar to cytokinin oxidase/dehydrogenase, which catalyzes the degradation of cytokinins. |
| HanXRQr2_Chr10g0455621 | 2.422387 | 0.0053805 | LUPEOL SYNTHASE 2 (ATLUP2);LUPEOL SYNTHASE 2 (LUP2) | Encodes a multifunctional 2-3-oxidosqualene (OS)-triterpene cyclase that can cyclize OS into lupeol, alpha- and beta-amyrin. |
| HanXRQr2_Chr13g0577061 | 2.029859 | 0.0054509 | BRASSINOSTEROID-RESPONSIVE RING-H2 (BRH1) | Encodes a novel ring finger protein and forms an N-terminal hydrophobic domain and a C-terminal RING-H2 signature. Expression is down regulated by brassinolide. |
| HanXRQr2_Chr04g0159101 | -2.043480 | 0.0056764 | 0 | Class-II DAHP synthetase family protein;(source:Araport11) |
| HanXRQr2_Chr14g0626641 | 2.796091 | 0.0065466 | PUMILIO 1 (PUM1);PUMILIO 1 (APUM1) | Encodes a member of the Arabidopsis Pumilio (APUM) proteins containing PUF domain (eight repeats of approximately 36 amino acids each). PUF proteins regulate both mRNA stability and translation through sequence-specific binding to the 3’ UTR of target mRNA transcripts. |
| HanXRQr2_Chr02g0047981 | 3.968239 | 0.0065502 | 0 | alpha/beta-Hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr08g0342131 | 4.880260 | 0.0075736 | LACCASE 1 (LAC1); (ATLAC1) | putative laccase, a member of laccase family of genes (with 17 members in Arabidopsis). |
| HanXRQr2_Chr15g0692621 | -2.072998 | 0.0092868 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr01g0029451 | 1.139352 | 0.0105256 | HISTONE DEACETYLASE 9 (HDA9); (HDA09); (ATHDAC9);HISTONE DEACETYLASE 9 (HDAC9); (ATHDA9) | Encodes HDA9 (a RPD3-like histone deacetylase). Functions in promoting the onset of leaf senescence.The hda9 mutant shows enhanced H3K9 acetylation levels,based on immunodetection using H3K9ac antibodies. |
| HanXRQr2_Chr16g0763511 | 2.017067 | 0.0110329 | (ATSTE14); (STE14);HOMOLOG OF YEAST STE14 A (ATSTE14A);HOMOLOG OF YEAST STE14 A (STE14A);ARABIDOPSIS THALIANA ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ATICMTA);ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ICMTA);LPHA-CARBOXYL METHYLTRANSFERASE (ATPCM) | Encodes a prenylcysteine alpha-carboxyl methyltransferase involved in methylation of isoprenylated proteins. This protein appears to have lower catalytic activity and a lower transcript expression level than the other ICMT present in Arabidopsis (At5g08335). Analysis of ICMT RNAi lines suggests that this protein may be involved in flower and stem development. |
| HanXRQr2_Chr04g0160801 | -1.053877 | 0.0116957 | TANDEM ZINC FINGER PROTEIN 9 (TZF9) | zinc finger (CCCH-type) family protein;(source:Araport11) |
| HanXRQr2_Chr04g0181821 | -2.598208 | 0.0129767 | TILLER ANGLE CONTROL 1 (TAC1) | Encodes TAC1 (Tiller Angle Control 1). Influences axillary branch growth angle. Inflorescence stems of TAC1 mutants are vertically oriented and have axillary shoots with narrow branch angles. |
| HanXRQr2_Chr03g0094331 | 2.092500 | 0.0131084 | IBH1-LIKE 1 (IBL1) | sequence-specific DNA binding transcription factor;(source:Araport11) |
| HanXRQr2_Chr04g0159131 | 1.648140 | 0.0134667 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0405521 | 6.251666 | 0.0138891 | CLAVATA 1 (CLV1); (ATCLV1);FLOWER DEVELOPMENT 5 (FLO5);FASCIATA 3 (FAS3) | Putative receptor kinase with an extracellular leucine-rich domain. Controls shoot and floral meristem size, and contributes to establish and maintain floral meristem identity. Negatively regulated by KAPP (kinase-associated protein phosphatase). CLV3 peptide binds directly CLV1 ectodomain. |
| HanXRQr2_Chr02g0051511 | 1.158735 | 0.0174447 | DEFECTIVE IN MERISTEM SILENCING 11 (DMS11); (ATMORC6);MICRORCHIDIA 6 (MORC6) | Encodes a member of the conserved Microrchidia (MORC) adenosine triphosphatase (ATPase) family, predicted to catalyze alterations in chromosome superstructure. Required for heterochromatin condensation and gene silencing. |
| HanXRQr2_Chr12g0560991 | 1.647297 | 0.0174986 | NA | ER membrane protein, putative (DUF962) |
| HanXRQr2_Chr01g0024991 | -1.784250 | 0.0201737 | ACA1 | Encodes a chloroplast envelope Ca2+-ATPase with an N-terminal autoinhibitor. |
| HanXRQr2_Chr14g0639041 | -1.304650 | 0.0224557 | ABS2 | AP2/B3-like transcriptional factor family protein |
| HanXRQr2_Chr14g0656381 | -3.630458 | 0.0226400 | ATMYB38, BIT1, BLUE INSENSITIVE TRAIT 1, MYB DOMAIN PROTEIN 38, MYB38, RAX2, REGULATOR OF AXILLARY MERISTEMS 2 | “Putative homolog of the Blind gene in tomato. Together with RAX1 and RAX3 belong to the class R2R3 MYB genes; encoded by the Myb-like transcription factor MYB38, regulates axillary meristem formation.” The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0160551 | 3.652872 | 0.0257605 | WOUND-INDUCED POLYPEPTIDE 3 (WIP3) | Member of the wound-induced polypeptide (WIP) family. |
| HanXRQr2_Chr09g0372751 | -3.034692 | 0.0301076 | NA | Glycosyl hydrolase family 10 protein |
| HanXRQr2_Chr03g0127971 | 1.808420 | 0.0325873 | (BHLH014); (BHLH14) | bHLH14 interacts with JAZ proteins, and functions redundantly with bHLH3, bHLH13 and bHLH17 to negatively regulate jasmonate responses. |
| HanXRQr2_Chr14g0627041 | 1.347879 | 0.0328480 | CYCLIC NUCLEOTIDE-BINDING TRANSPORTER 1 (CNBT1);CYCLIC NUCLEOTIDE GATED CHANNEL 20 (CNGC20);CYCLIC NUCLEOTIDE-GATED CHANNEL 20 (ATCNGC20) | cyclic nucleotide-binding transporter 1, member of a family of cyclic nucleotide gated channels. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0158921 | 1.361491 | 0.0340022 | BETA-XYLOSIDASE 2 (ATBXL2);BETA-XYLOSIDASE 2 (BXL2) | encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members. |
| HanXRQr2_Chr09g0415751 | 1.317503 | 0.0367323 | GATA TRANSCRIPTION FACTOR 12 (GATA12) | Encodes a member of the GATA factor family of zinc finger transcription factors. |
| HanXRQr2_Chr14g0670511 | -4.735777 | 0.0381361 | MUTE (MUTE) | Encodes a basic helix-loop-helix (bHLH) protein that controls meristemoid differentiation during stomatal development. In the absence of MUTE, meristemoids abort after excessive asymmetric divisions and fail to differentiate stomata. MUTE expression in the meristemoid is required for SLGCs differentiation as pavement cells. Epidermal cells lose their competence to respond to MUTE overexpression during cotyledon development. |
| HanXRQr2_Chr06g0256251 | -1.834243 | 0.0382253 | NA | pentatricopeptide (PPR) repeat-containing protein;(source:Araport11) |
| HanXRQr2_Chr11g0485451 | -3.685649 | 0.0440644 | UDP-GLUCOSYL TRANSFERASE 85A3 (AtUGT85A3);UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) | Encodes a putative UDP-glucosyl transferase. At1g22380 was initially identified as encoding the protein AAF87154, which has been classified as a bHLH protein (AtbHLH152). Subsequently it has been found that the AAF87154 protein appears to be encoded by the AT1G23970 genomic locus. |
1.3 Node
plot.volcano(overlap.node)
kable.overlap(overlap.node)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 8.437615 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 6.767897 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 8.457146 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 4.547802 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr02g0059761 | -4.438978 | 0.0000000 | ARABIDOPSIS THALIANA PEPTIDE TRANSPORTER 1 (ATPTR1); (ATNPF8.1);NRT1/ PTR FAMILY 8.1 (NPF8.1);PEPTIDE TRANSPORTER 1 (PTR1) | Encodes a di- and tri-peptide transporter that recognizes a variety of different amino acid combinations. GFP-tagged PTR1 localizes to the plasma membrane and has 8 to 11 predicted transmembrane domains. PTR1 is expressed in a number of different vascular tissues throughout the plant based on promoter:GUS expression analysis. ptr1 mutants have a lower dry weight than wild type plants when both are grown with Pro-Ala or Ala-Ala dipeptides as their nitrogen source, suggesting that PTR1 plays a role in dipeptide uptake in the roots. Furthermore N content of ptr1 mutants is lower than that of wild type plants when grown with Pro-Ala or a mixture of dipeptides as nitrogen source |
| HanXRQr2_Chr05g0230361 | 4.875310 | 0.0000003 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr07g0311551 | 9.216151 | 0.0000006 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr16g0749261 | 6.233158 | 0.0000022 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr10g0442521 | -3.338361 | 0.0000033 | (B120) | S-locus lectin protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr12g0549501 | -1.118512 | 0.0000048 | NA | NA |
| HanXRQr2_Chr17g0781641 | -2.352825 | 0.0000340 | AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 21 (AHL21);GIANT KILLER (GIK) | Direct target of AGAMOUS. Regulates patterning and differentiation of reproductive organs. |
| HanXRQr2_Chr14g0659991 | -3.364918 | 0.0000640 | ANGUSTIFOLIA 3 (AN3);GRF1-INTERACTING FACTOR (GIF);ARABIDOPSIS GRF1-INTERACTING FACTOR 1 (ATGIF1);GRF1-INTERACTING FACTOR 1 (GIF1) | Encodes a protein with similarity to mammalian transcriptional coactivator that is involved in cell proliferation during leaf and flower development. Loss of function mutations have narrow, pointed leaves and narrow floral organs. AN3 interacts with members of the growth regulating factor (GRF) family of transcription factors. |
| HanXRQr2_Chr09g0381571 | 1.967476 | 0.0000648 | 0 | NAD(P)-binding Rossmann-fold superfamily protein;(source:Araport11) |
| HanXRQr2_Chr06g0261551 | 4.459540 | 0.0001303 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr12g0533611 | -1.136575 | 0.0001357 | 0 | CDK inhibitor P21 binding protein;(source:Araport11) |
| HanXRQr2_Chr10g0430021 | -4.869082 | 0.0001685 | ATGPAT6, GLYCEROL-3-PHOSPHATE SN-2-ACYLTRANSFERASE 6, GPAT6 | bifunctional sn-glycerol-3-phosphate 2-O-acyltransferase/phosphatase. Involved in cutin assembly. |
| HanXRQr2_Chr06g0274391 | -2.747971 | 0.0001930 | CUTIN SYNTHASE2 (CUS2) | GDSL-motif esterase/acyltransferase/lipase. Enzyme group with broad substrate specificity that may catalyze acyltransfer or hydrolase reactions with lipid and non-lipid substrates. Mutants are defective in cuticle formation with reduced sepal cuticle ridge formation. |
| HanXRQr2_Chr06g0258881 | -1.102550 | 0.0004700 | DISPROPORTIONATING ENZYME 2 (DPE2) | Encodes a cytosolic protein with transglucosidase and amylomaltase activity. It is an essential component of the pathway from starch to sucrose and cellular metabolism in leaves at night. The protein binds to heteroglycans and utilizes glucose, mannose and xylose as acceptors. Fucose and galactose can also act as acceptors but less efficiently than the previous three. It was also was also recently reported to act on maltodextrins. On the other hand, arabinose and fructose were not efficiently used. Its role probably includes metabolizing maltose exported from the chloroplast. Studies using maltose extracted from the double mutant be2-1 be3-2 showed that this enzyme is preferentially active of β-maltose. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr03g0127681 | -2.806380 | 0.0005110 | (NUP98A);DRACULA2 (DRA2) | DRA2 is a homolog of mammalian nucleoporin 98 and a likely component of the nuclear pore complex in Arabidopsis. It positively participates in the control of the hypocotyl elongation response to plant proximity and control of shade induced gene expression. Nucleoportin which redundantly inhibits flowering together with Nup98b through multiple pathways including clock, photoperiod, and age pathways. Gates flowering in a CONSTANS (CO)-independent mode and bypasses the CO checkpoint in photoperiodic signaling and integrated signals from multiple pathways to directly target FLOWERING LOCUS T (FT) for flowering control. |
| HanXRQr2_Chr07g0292811 | 2.580169 | 0.0006051 | NA | NA |
| HanXRQr2_Chr05g0227611 | -3.109375 | 0.0007351 | ATSWEET10, SWEET10 | Encodes a member of the SWEET sucrose efflux transporter family proteins. |
| HanXRQr2_Chr09g0409291 | 3.519831 | 0.0008905 | ABA-IMPORTING TRANSPORTER 1, AIT1, ATNPF4.6, ATNRT1:2, NITRATE TRANSPORTER 1:2, NPF4.6, NRT1.2, NRT1/ PTR FAMILY 4.6, NRT1:2, NTL1 | Encodes an inducible component of low-affinity nitrate uptake. mRNA found primarily in root hairs and the epidermis of roots. It also acts as an ABA importer at the site of ABA biosynthesis and is important for the regulation of stomatal aperture in inflorescence stems. |
| HanXRQr2_Chr04g0160391 | -6.058849 | 0.0012587 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr11g0475771 | -4.299112 | 0.0012702 | LYSM RLK1-INTERACTING KINASE 1 (LIK1) | Encodes LRR-RLK protein that is localized to the plasma membrane and is involved in regulation of plant innate immunity to microbes. LIK1 is phosphorylated by CERK1, a kinase involved in chitin perception. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0380251 | -2.931990 | 0.0019526 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr06g0241401 | -2.481282 | 0.0020893 | TARGET OF MONOPTEROS 3 (TMO3);CYTOKININ RESPONSE FACTOR 2 (CRF2) | encodes a member of the ERF (ethylene response factor) subfamily B-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 7 members in this subfamily. Monopteros target gene. CRF proteins relocalize to the nucleus in response to cytokinin. |
| HanXRQr2_Chr09g0362371 | -3.615766 | 0.0021149 | NA | NA |
| HanXRQr2_Chr09g0372471 | -3.108005 | 0.0023013 | ATHPT, HOMOGENTISATE PHYTYLTRANSFERASE, HOMOGENTISATE PHYTYLTRANSFERASE 1, HPT1, TPT1, VITAMIN E 2, VTE2 | Encodes homogentisate phytyltransferase involved in tocopherol biosynthesis. Has impact on seed longevity and plays a role in the adaptation to low temperature stress, notably phloem loading. |
| HanXRQr2_Chr15g0689291 | 3.964008 | 0.0037964 | GLABROUS INFLORESCENCE STEMS 3 (GIS3) | Encodes a nuclear localized member of the C2H2 family of TFIIIA transcription factors.GIS3 is involved in trichome initiation and development downstream of GA and cytokinin signaling. GIS regulates the expression GIS and GIS2. |
| HanXRQr2_Chr15g0686631 | -4.235576 | 0.0039074 | ATBZIP42, BASIC LEUCINE-ZIPPER 42, BZIP42 | basic leucine-zipper 42 |
| HanXRQr2_Chr04g0159101 | -2.109512 | 0.0043077 | 0 | Class-II DAHP synthetase family protein;(source:Araport11) |
| HanXRQr2_Chr04g0181821 | -3.135267 | 0.0048008 | TILLER ANGLE CONTROL 1 (TAC1) | Encodes TAC1 (Tiller Angle Control 1). Influences axillary branch growth angle. Inflorescence stems of TAC1 mutants are vertically oriented and have axillary shoots with narrow branch angles. |
| HanXRQr2_Chr10g0453001 | -1.769912 | 0.0053494 | “COLD, CIRCADIAN RHYTHM, AND RNA BINDING 2”, ATGRP7, CCR2, GLYCINE RICH PROTEIN 7, GLYCINE-RICH RNA-BINDING PROTEIN 7, GR-RBP7, GRP7, RBGA3, RNA-BINDING GLYCINE-RICH PROTEIN A3 | Encodes a small glycine-rich RNA binding protein that is part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript. Gene expression is induced by cold. GRP7 appears to promote stomatal opening and reduce tolerance under salt and dehydration stress conditions, but, promotes stomatal closing and thereby increases stress tolerance under conditions of cold tolerance. Loss of function mutations have increased susceptibility to pathogens suggesting a role in mediating innate immune response. Mutants are also late flowering in a non-photoperiodic manner and are responsive to vernalization suggesting an interaction with the autonomous flowering pathway. There is a reduction of mRNA export from the nucleus in grp7 mutants. GRP7:GFP fusion proteins can be found in the cytosol and nucleus. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase). |
| HanXRQr2_Chr12g0553211 | -4.228337 | 0.0058410 | WUSCHEL RELATED HOMEOBOX 1 (WOX1) | Encodes a WUSCHEL-related homeobox gene family member with 65 amino acids in its homeodomain. Proteins in this family contain a sequence of eight residues (TLPLFPMH) downstream of the homeodomain called the WUS box. Its mRNA is expressed in the initiating vascular primordium of the cotyledons during heart and torpedo stages. |
| HanXRQr2_Chr03g0127971 | -2.269426 | 0.0059981 | (BHLH014); (BHLH14) | bHLH14 interacts with JAZ proteins, and functions redundantly with bHLH3, bHLH13 and bHLH17 to negatively regulate jasmonate responses. |
| HanXRQr2_Chr14g0626321 | -4.677522 | 0.0061405 | 0 | Terpenoid cyclases/Protein prenyltransferases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr04g0160711 | -4.149833 | 0.0092553 | GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (ASN1);ARABIDOPSIS THALIANA GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (AT-ASN1);DARK INDUCIBLE 6 (DIN6) | encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene’s expression pattern is responding to the level of sugar in the cell. |
| HanXRQr2_Chr15g0698701 | -1.591068 | 0.0098602 | NA | Dof-type zinc finger DNA-binding family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 2.323278 | 0.0112566 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 2.323278 | 0.0112566 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr12g0552691 | 1.526056 | 0.0116592 | IRX15-LIKE (IRX15-L) | Encode a DUF579 (domain of unknown function 579) containing protein essential for normal xylan synthesis and deposition in the secondary cell wall. |
| HanXRQr2_Chr04g0159131 | -1.634892 | 0.0119309 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0284351 | 2.050416 | 0.0122990 | ANAC043, ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 43, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1, NST1 | NAC transcription factor NST1. NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls and siliques. An NST1 promoter fusion was detected in various tissues in which lignified secondary walls develop. Both MYC2 and MYC4 bind to the NST1 promoter and appear to regulate its expression in response to blue light. |
| HanXRQr2_Chr11g0474921 | -2.490406 | 0.0148391 | ARABIDOPSIS THALIANA GIBBERELLIN 2-OXIDASE 1, ATGA2OX1, GA2OX1, GIBBERELLIN 2-OXIDASE 1 | Encodes a gibberellin 2-oxidase that acts on C19 gibberellins. |
| HanXRQr2_Chr04g0149371 | -2.501670 | 0.0148545 | CYTOCHROME P450, FAMILY 71, SUBFAMILY A, POLYPEPTIDE 22 (CYP71A22) | putative cytochrome P450 |
| HanXRQr2_Chr16g0731771 | -1.080974 | 0.0162725 | 0 | RING/U-box superfamily protein;(source:Araport11) |
| HanXRQr2_Chr04g0159711 | 2.103838 | 0.0181959 | EXPANSIN A1 (ATEXPA1);EXPANSIN 1 (EXP1);EXPANSIN A1 (EXPA1); (ATEXP1); (ATHEXP ALPHA 1.2); (AT-EXP1) | Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. |
| HanXRQr2_Chr11g0476951 | -1.740671 | 0.0186973 | CUP-SHAPED COTYLEDON 2 (CUC2);CUP-SHAPED COTYLEDON 2 (ATCUC2);ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 98 (ANAC098) | Transcriptional activator of the NAC gene family, with CUC1 redundantly required for embryonic apical meristem formation, cotyledon separation and expression of STM. Proper timing of CUC2 expression is required to maintain the phyllotactic pattern initiated in the meristem. CUC2 expression in leaf sinus region is required for serration and the extent of serration is modulated by mir164A mediated repression of CUC2. |
| HanXRQr2_Chr12g0552841 | -1.092882 | 0.0209789 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr11g0476841 | -1.535080 | 0.0215893 | (BZIP61); (ATBZIP61) | Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP34. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells. |
| HanXRQr2_Chr04g0158921 | 1.276270 | 0.0238340 | BETA-XYLOSIDASE 2 (ATBXL2);BETA-XYLOSIDASE 2 (BXL2) | encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members. |
| HanXRQr2_Chr14g0644791 | -4.655493 | 0.0248596 | CYSTEINE-RICH RLK (RECEPTOR-LIKE PROTEIN KINASE) 3 (CRK3) | Encodes a cysteine-rich receptor-like protein kinase. |
| HanXRQr2_Chr10g0423291 | -1.286361 | 0.0249796 | (H2A.Z);HISTONE H2A 11 (HTA11) | Encodes HTA11, a histone H2A protein. Loss of all H2A.Z (triple mutant with HTA8 and HTA9) results in a reduction in DNA methylation of transposons but not that of genes. Loss of H2A.Z causes misregulation of many genes involved in the response to developmental and environmental cues, and that these genes tend to have high levels of gene-body H2A.Z. |
| HanXRQr2_Chr15g0693421 | -4.195234 | 0.0254557 | (GH3-10);DWARF IN LIGHT 2 (DFL2) | Encodes a GH3-related gene involved in red light-specific hypocotyl elongation. Analysis of sense and antisense transgenic plants suggests that DFL2 is located downstream of red light signal transduction and determines the degree of hypocotyl elongation. |
| HanXRQr2_Chr16g0776431 | -2.147378 | 0.0286098 | SMALL AUXIN UPREGULATED RNA 12 (SAUR12) | SAUR-like auxin-responsive protein family;(source:Araport11) |
| HanXRQr2_Chr14g0663681 | -1.021138 | 0.0293809 | PSEUDO-RESPONSE REGULATOR 3 (PRR3) | Encodes pseudo-response regulator 3 (APRR3/PRR3). PRR3 transcript levels vary in a circadian pattern with peak expression at dusk under long and short day conditions. PRR3 affects the period of the circadian clock and seedlings with reduced levels of PRR3 have shorter periods, based on transcriptional assays of clock-regulated genes. PRR3 is expressed in the vasculature of cotyledons and leaves where it may help stabilize the TOC1 protein by preventing interactions between TOC1 and the F-box protein ZTL. |
| HanXRQr2_Chr09g0405521 | 5.155002 | 0.0307064 | CLAVATA 1 (CLV1); (ATCLV1);FLOWER DEVELOPMENT 5 (FLO5);FASCIATA 3 (FAS3) | Putative receptor kinase with an extracellular leucine-rich domain. Controls shoot and floral meristem size, and contributes to establish and maintain floral meristem identity. Negatively regulated by KAPP (kinase-associated protein phosphatase). CLV3 peptide binds directly CLV1 ectodomain. |
| HanXRQr2_Chr09g0409311 | -1.069945 | 0.0340783 | ARABIDOPSIS THALIANA HOMEOBOX 1, ATHB-1, ATHB1, CONSERVED PEPTIDE UPSTREAM OPEN READING FRAME 33, CPUORF33, HAT5, HB-1, HD-ZIP-1, HOMEOBOX 1, HOMEODOMAIN PROTEIN FROM ARABIDOIPSIS THALIANA 5 | Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf and hypocotyl development. Its promoter is bound by PIF1 which likely regulates its expression. Its translation is regulated by a conserved upstream ORF (CPuORF33) |
| HanXRQr2_Chr09g0372751 | -2.945040 | 0.0369319 | NA | Glycosyl hydrolase family 10 protein |
| HanXRQr2_Chr10g0442381 | -2.678468 | 0.0389591 | SERINE HYDROXYMETHYLTRANSFERASE 6 (SHM6) | Encodes a putative serine hydroxymethyltransferase. |
| HanXRQr2_Chr08g0336101 | -3.506979 | 0.0396171 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr11g0518021 | -2.805266 | 0.0428604 | YUCCA 1 (YUC1);YUCCA (YUC) | Mutant has elevated levels of free IAA in dominant mutant allele; Flavin Monooxygenase-Like Enzyme; Auxin Biosynthesis |
| HanXRQr2_Chr11g0485451 | -4.082192 | 0.0455144 | UDP-GLUCOSYL TRANSFERASE 85A3 (AtUGT85A3);UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) | Encodes a putative UDP-glucosyl transferase. At1g22380 was initially identified as encoding the protein AAF87154, which has been classified as a bHLH protein (AtbHLH152). Subsequently it has been found that the AAF87154 protein appears to be encoded by the AT1G23970 genomic locus. |
| HanXRQr2_Chr13g0593361 | 1.953929 | 0.0472159 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
1.4 Leaf
plot.volcano(overlap.leaf)
kable.overlap(overlap.leaf)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 6.797932 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 7.258738 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 8.942354 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr14g0670491 | 1.586734 | 0.0000005 | EMBRYO DEFECTIVE 9 (EMB9);DHFS-FPGS HOMOLOG A (DFA);A. THALIANA DHFS-FPGS HOMOLOG A (ATDFA);GLOBULAR ARREST1 (GLA1) | Encodes a dihydrofolate synthetase based on yeast complementation experiments. This protein is involved in folate biosynthesis. |
| HanXRQr2_Chr05g0230361 | 5.409148 | 0.0000013 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr04g0160001 | 3.823981 | 0.0000036 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0311551 | 9.612150 | 0.0000085 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr10g0423291 | -3.345864 | 0.0000148 | (H2A.Z);HISTONE H2A 11 (HTA11) | Encodes HTA11, a histone H2A protein. Loss of all H2A.Z (triple mutant with HTA8 and HTA9) results in a reduction in DNA methylation of transposons but not that of genes. Loss of H2A.Z causes misregulation of many genes involved in the response to developmental and environmental cues, and that these genes tend to have high levels of gene-body H2A.Z. |
| HanXRQr2_Chr09g0372471 | -5.529771 | 0.0000218 | ATHPT, HOMOGENTISATE PHYTYLTRANSFERASE, HOMOGENTISATE PHYTYLTRANSFERASE 1, HPT1, TPT1, VITAMIN E 2, VTE2 | Encodes homogentisate phytyltransferase involved in tocopherol biosynthesis. Has impact on seed longevity and plays a role in the adaptation to low temperature stress, notably phloem loading. |
| HanXRQr2_Chr16g0749261 | 6.076711 | 0.0000258 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr07g0311941 | 4.193939 | 0.0000584 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 4.193939 | 0.0000584 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0303621 | 1.069291 | 0.0002001 | NA | NA |
| HanXRQr2_Chr12g0533611 | -1.135334 | 0.0003944 | 0 | CDK inhibitor P21 binding protein;(source:Araport11) |
| HanXRQr2_Chr04g0159711 | 4.189014 | 0.0004840 | EXPANSIN A1 (ATEXPA1);EXPANSIN 1 (EXP1);EXPANSIN A1 (EXPA1); (ATEXP1); (ATHEXP ALPHA 1.2); (AT-EXP1) | Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. |
| HanXRQr2_Chr04g0166021 | -3.308066 | 0.0005973 | Participates with ELO2 in VLCFA synthesis. | fatty acid biosynthesis |
| HanXRQr2_Chr09g0362371 | -3.452481 | 0.0012670 | NA | NA |
| HanXRQr2_Chr03g0127681 | -7.159142 | 0.0013000 | (NUP98A);DRACULA2 (DRA2) | DRA2 is a homolog of mammalian nucleoporin 98 and a likely component of the nuclear pore complex in Arabidopsis. It positively participates in the control of the hypocotyl elongation response to plant proximity and control of shade induced gene expression. Nucleoportin which redundantly inhibits flowering together with Nup98b through multiple pathways including clock, photoperiod, and age pathways. Gates flowering in a CONSTANS (CO)-independent mode and bypasses the CO checkpoint in photoperiodic signaling and integrated signals from multiple pathways to directly target FLOWERING LOCUS T (FT) for flowering control. |
| HanXRQr2_Chr07g0284941 | -3.219145 | 0.0015477 | CYCLIN A2;1 (CYCA2;1) | core cell cycle genes |
| HanXRQr2_Chr06g0261551 | 3.771938 | 0.0016372 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr15g0706001 | -2.401048 | 0.0017467 | AGAMOUS-LIKE 22, AGL22, FAQ1, FLOWERING ARABIDOPSIS QTL1, SHORT VEGETATIVE PHASE, SVP | Encodes a nuclear protein that acts as a floral repressor and that functions within the thermosensory pathway. SVP represses FT expression via direct binding to the vCArG III motif in the FT promoter. |
| HanXRQr2_Chr12g0550641 | 1.464225 | 0.0069536 | LOB DOMAIN-CONTAINING PROTEIN 41 (LBD41) | LOB domain-containing protein 41;(source:Araport11) |
| HanXRQr2_Chr02g0059761 | -1.834667 | 0.0098447 | ARABIDOPSIS THALIANA PEPTIDE TRANSPORTER 1 (ATPTR1); (ATNPF8.1);NRT1/ PTR FAMILY 8.1 (NPF8.1);PEPTIDE TRANSPORTER 1 (PTR1) | Encodes a di- and tri-peptide transporter that recognizes a variety of different amino acid combinations. GFP-tagged PTR1 localizes to the plasma membrane and has 8 to 11 predicted transmembrane domains. PTR1 is expressed in a number of different vascular tissues throughout the plant based on promoter:GUS expression analysis. ptr1 mutants have a lower dry weight than wild type plants when both are grown with Pro-Ala or Ala-Ala dipeptides as their nitrogen source, suggesting that PTR1 plays a role in dipeptide uptake in the roots. Furthermore N content of ptr1 mutants is lower than that of wild type plants when grown with Pro-Ala or a mixture of dipeptides as nitrogen source |
| HanXRQr2_Chr12g0552841 | -1.280509 | 0.0115851 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr14g0656381 | -3.553691 | 0.0155146 | ATMYB38, BIT1, BLUE INSENSITIVE TRAIT 1, MYB DOMAIN PROTEIN 38, MYB38, RAX2, REGULATOR OF AXILLARY MERISTEMS 2 | “Putative homolog of the Blind gene in tomato. Together with RAX1 and RAX3 belong to the class R2R3 MYB genes; encoded by the Myb-like transcription factor MYB38, regulates axillary meristem formation.” The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr13g0593361 | 2.689179 | 0.0170835 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr04g0161431 | 1.696026 | 0.0184853 | ATMYB59, ATMYB59-1, ATMYB59-2, ATMYB59-3, MYB DOMAIN PROTEIN 59, MYB59 | Encodes a putative transcription factor (MYB59). |
| HanXRQr2_Chr12g0553211 | -6.439910 | 0.0189513 | WUSCHEL RELATED HOMEOBOX 1 (WOX1) | Encodes a WUSCHEL-related homeobox gene family member with 65 amino acids in its homeodomain. Proteins in this family contain a sequence of eight residues (TLPLFPMH) downstream of the homeodomain called the WUS box. Its mRNA is expressed in the initiating vascular primordium of the cotyledons during heart and torpedo stages. |
| HanXRQr2_Chr08g0339271 | -2.967462 | 0.0194559 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr05g0216981 | -1.349001 | 0.0194914 | 0 | Pyruvate kinase family protein;(source:Araport11) |
| HanXRQr2_Chr09g0380251 | -2.523322 | 0.0196941 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr13g0579691 | -1.245232 | 0.0219147 | GATA TRANSCRIPTION FACTOR 15 (GATA15) | Encodes a member of the GATA factor family of zinc finger transcription factors. |
| HanXRQr2_Chr04g0160391 | -4.569024 | 0.0242154 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr11g0479121 | 1.516194 | 0.0272929 | PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) | Member of GRAS gene family. Semi-dominant mutant has a reduced response to far-red light and appears to act early in the phytochrome A signaling pathway. |
| HanXRQr2_Chr11g0476951 | -2.072993 | 0.0274021 | CUP-SHAPED COTYLEDON 2 (CUC2);CUP-SHAPED COTYLEDON 2 (ATCUC2);ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 98 (ANAC098) | Transcriptional activator of the NAC gene family, with CUC1 redundantly required for embryonic apical meristem formation, cotyledon separation and expression of STM. Proper timing of CUC2 expression is required to maintain the phyllotactic pattern initiated in the meristem. CUC2 expression in leaf sinus region is required for serration and the extent of serration is modulated by mir164A mediated repression of CUC2. |
| HanXRQr2_Chr10g0442521 | -1.427999 | 0.0311748 | (B120) | S-locus lectin protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr09g0416891 | -1.052352 | 0.0325743 | 0 | Protein kinase superfamily protein;(source:Araport11) |
| HanXRQr2_Chr07g0294491 | 1.551375 | 0.0334736 | 0 | RING/U-box superfamily protein;(source:Araport11) |
| HanXRQr2_Chr16g0744931 | 1.609483 | 0.0339683 | ARABIDOPSIS THALIANA TONOPLAST INTRINSIC PROTEIN 2;3 (ATTIP2;3);TONOPLAST INTRINSIC PROTEIN 2;3 (TIP2;3);DELTA-TONOPLAST INTRINSIC PROTEIN 3 (DELTA-TIP3) | Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3). |
| HanXRQr2_Chr03g0127971 | 2.080177 | 0.0396202 | (BHLH014); (BHLH14) | bHLH14 interacts with JAZ proteins, and functions redundantly with bHLH3, bHLH13 and bHLH17 to negatively regulate jasmonate responses. |
| HanXRQr2_Chr02g0051511 | -1.700146 | 0.0412580 | DEFECTIVE IN MERISTEM SILENCING 11 (DMS11); (ATMORC6);MICRORCHIDIA 6 (MORC6) | Encodes a member of the conserved Microrchidia (MORC) adenosine triphosphatase (ATPase) family, predicted to catalyze alterations in chromosome superstructure. Required for heterochromatin condensation and gene silencing. |
| HanXRQr2_Chr01g0017161 | 3.126172 | 0.0446698 | LIGHT SENSITIVE HYPOCOTYLS 6 (LSH6) | LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640);(source:Araport11) |
| HanXRQr2_Chr06g0256251 | -2.241989 | 0.0478592 | NA | pentatricopeptide (PPR) repeat-containing protein;(source:Araport11) |
1.5 Meristem
plot.volcano(overlap.meristem)
kable.overlap(overlap.meristem)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 8.352397 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 5.133290 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 8.336782 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 5.447798 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0311551 | 9.445977 | 0.0000004 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr16g0749261 | 7.018134 | 0.0000008 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr05g0230361 | 4.435068 | 0.0000012 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr04g0165351 | -1.298928 | 0.0000036 | NA | hypothetical protein;(source:Araport11) |
| HanXRQr2_Chr04g0159131 | -3.235749 | 0.0000239 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0372471 | -7.233106 | 0.0001036 | ATHPT, HOMOGENTISATE PHYTYLTRANSFERASE, HOMOGENTISATE PHYTYLTRANSFERASE 1, HPT1, TPT1, VITAMIN E 2, VTE2 | Encodes homogentisate phytyltransferase involved in tocopherol biosynthesis. Has impact on seed longevity and plays a role in the adaptation to low temperature stress, notably phloem loading. |
| HanXRQr2_Chr04g0159711 | 6.033504 | 0.0001399 | EXPANSIN A1 (ATEXPA1);EXPANSIN 1 (EXP1);EXPANSIN A1 (EXPA1); (ATEXP1); (ATHEXP ALPHA 1.2); (AT-EXP1) | Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. |
| HanXRQr2_Chr15g0692621 | 3.053564 | 0.0001422 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr06g0261551 | 3.964740 | 0.0004285 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr12g0533581 | -2.122585 | 0.0005215 | CHLORORESPIRATORY REDUCTION 23 (CRR23);NADH DEHYDROGENASE-LIKE COMPLEX L (NdhL) | a subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in PSI cyclic electron transport. Located on the thylakoid membrane. Mutant has impaired NAD(P)H dehydrogenase activity. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr15g0708701 | -3.375206 | 0.0006181 | NITRATE REDUCTASE 2 (NIA2); (B29); (NIA2-1);ARABIDOPSIS NITRATE REDUCTASE 2 (ATNR2);NITRATE REDUCTASE (NR);NITRATE REDUCTASE 2 (NR2);CHLORATE RESISTANT 3 (CHL3) | Identified as a mutant resistant to chlorate. Encodes nitrate reductase structural gene. Involved in nitrate assimilation. Has nitrate reductase activity. Up-regulated by the fungus P. indica. Binds transcription factor At2g35940. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0311941 | 3.078718 | 0.0008717 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 3.078718 | 0.0008717 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr04g0159101 | -2.413677 | 0.0013558 | 0 | Class-II DAHP synthetase family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160391 | -6.266041 | 0.0015709 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr09g0409311 | -1.701993 | 0.0020087 | ARABIDOPSIS THALIANA HOMEOBOX 1, ATHB-1, ATHB1, CONSERVED PEPTIDE UPSTREAM OPEN READING FRAME 33, CPUORF33, HAT5, HB-1, HD-ZIP-1, HOMEOBOX 1, HOMEODOMAIN PROTEIN FROM ARABIDOIPSIS THALIANA 5 | Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf and hypocotyl development. Its promoter is bound by PIF1 which likely regulates its expression. Its translation is regulated by a conserved upstream ORF (CPuORF33) |
| HanXRQr2_Chr14g0663681 | -1.421688 | 0.0027519 | PSEUDO-RESPONSE REGULATOR 3 (PRR3) | Encodes pseudo-response regulator 3 (APRR3/PRR3). PRR3 transcript levels vary in a circadian pattern with peak expression at dusk under long and short day conditions. PRR3 affects the period of the circadian clock and seedlings with reduced levels of PRR3 have shorter periods, based on transcriptional assays of clock-regulated genes. PRR3 is expressed in the vasculature of cotyledons and leaves where it may help stabilize the TOC1 protein by preventing interactions between TOC1 and the F-box protein ZTL. |
| HanXRQr2_Chr08g0339271 | 1.828064 | 0.0049729 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr17g0796691 | 2.279657 | 0.0070618 | APETALA1 (AP1); (ATAP1);AGAMOUS-LIKE 7 (AGL7) | Floral homeotic gene encoding a MADS domain protein homologous to SRF transcription factors. Specifies floral meristem and sepal identity. Required for the transcriptional activation of AGAMOUS. Interacts with LEAFY.Binds to promoter and regulates the expression of flowering time genes SVP, SOC1 and AGL24. |
| HanXRQr2_Chr09g0380251 | -2.513714 | 0.0076717 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr09g0362371 | -2.570724 | 0.0097784 | NA | NA |
| HanXRQr2_Chr04g0166021 | -2.571532 | 0.0113943 | Participates with ELO2 in VLCFA synthesis. | fatty acid biosynthesis |
| HanXRQr2_Chr12g0552511 | -1.179970 | 0.0134739 | ATMYB73, MYB DOMAIN PROTEIN 73, MYB73 | Member of the R2R3 factor gene family. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0145031 | 1.752988 | 0.0158458 | SNF1-RELATED PROTEIN KINASE 3.24 (SnRK3.24);CBL-INTERACTING PROTEIN KINASE 5 (CIPK5) | Encodes CBL-interacting protein kinase 5 (CIPK5). |
| HanXRQr2_Chr11g0476841 | -1.606857 | 0.0160600 | (BZIP61); (ATBZIP61) | Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP34. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells. |
| HanXRQr2_Chr12g0560991 | 1.709976 | 0.0178114 | NA | ER membrane protein, putative (DUF962) |
| HanXRQr2_Chr04g0149371 | -2.466891 | 0.0192955 | CYTOCHROME P450, FAMILY 71, SUBFAMILY A, POLYPEPTIDE 22 (CYP71A22) | putative cytochrome P450 |
| HanXRQr2_Chr12g0555521 | -2.192455 | 0.0204654 | ATRING1, RING1 | Encodes a RING finger domain protein with E3 ligase activity that is localized to the lipid rafts of the plasma membrane. Expression is increased in response to fungal pathogen. May be involved in regulation of programmed cell death by facilitating degredation of regulation of PDC activators. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0731771 | -1.010154 | 0.0247089 | 0 | RING/U-box superfamily protein;(source:Araport11) |
| HanXRQr2_Chr12g0552841 | -1.067121 | 0.0248640 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr04g0181821 | -2.510426 | 0.0270206 | TILLER ANGLE CONTROL 1 (TAC1) | Encodes TAC1 (Tiller Angle Control 1). Influences axillary branch growth angle. Inflorescence stems of TAC1 mutants are vertically oriented and have axillary shoots with narrow branch angles. |
| HanXRQr2_Chr13g0593361 | 2.148169 | 0.0301332 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr15g0689291 | 2.836446 | 0.0313729 | GLABROUS INFLORESCENCE STEMS 3 (GIS3) | Encodes a nuclear localized member of the C2H2 family of TFIIIA transcription factors.GIS3 is involved in trichome initiation and development downstream of GA and cytokinin signaling. GIS regulates the expression GIS and GIS2. |
| HanXRQr2_Chr11g0509931 | 2.660057 | 0.0351987 | MEDOS 2 (MDS2) | Involved in growth adaptation upon exposure to metal ions. Contributes together with the other MDS genes to the complex network of CrRLK1Ls that positively and negatively affect growth. |
| HanXRQr2_Chr14g0644791 | -4.391580 | 0.0380355 | CYSTEINE-RICH RLK (RECEPTOR-LIKE PROTEIN KINASE) 3 (CRK3) | Encodes a cysteine-rich receptor-like protein kinase. |
| HanXRQr2_Chr10g0453001 | -1.302717 | 0.0434883 | “COLD, CIRCADIAN RHYTHM, AND RNA BINDING 2”, ATGRP7, CCR2, GLYCINE RICH PROTEIN 7, GLYCINE-RICH RNA-BINDING PROTEIN 7, GR-RBP7, GRP7, RBGA3, RNA-BINDING GLYCINE-RICH PROTEIN A3 | Encodes a small glycine-rich RNA binding protein that is part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript. Gene expression is induced by cold. GRP7 appears to promote stomatal opening and reduce tolerance under salt and dehydration stress conditions, but, promotes stomatal closing and thereby increases stress tolerance under conditions of cold tolerance. Loss of function mutations have increased susceptibility to pathogens suggesting a role in mediating innate immune response. Mutants are also late flowering in a non-photoperiodic manner and are responsive to vernalization suggesting an interaction with the autonomous flowering pathway. There is a reduction of mRNA export from the nucleus in grp7 mutants. GRP7:GFP fusion proteins can be found in the cytosol and nucleus. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase). |
| HanXRQr2_Chr11g0509401 | -5.972986 | 0.0458561 | ACH1, ATNRT2.1, ATNRT2:1, LATERAL ROOT INITIATION 1, LIN1, NITRATE TRANSPORTER 2, NITRATE TRANSPORTER 2.1, NITRATE TRANSPORTER 2:1, NRT2, NRT2.1, NRT2:1, NRT2;1AT | High-affinity nitrate transporter. Up-regulated by nitrate. Functions as a repressor of lateral root initiation independently of nitrate uptake. |
| HanXRQr2_Chr06g0274231 | 2.876695 | 0.0463686 | REDUCED STEM BRANCHING 8 (RSB8);FLOWERING LOCUS T (FT) | FT, together with LFY, promotes flowering and is antagonistic with its homologous gene, TERMINAL FLOWER1 (TFL1). Together with TSF, it plays an antagonistic role to TFL1 in the determination of inflorescence meristem identity. FT is expressed in leaves and is induced by long day treatment. Either the FT mRNA or protein is translocated to the shoot apex where it induces its own expression. Recent data suggests that FT protein acts as a long-range signal. FT is a target of CO and acts upstream of SOC1. |
1.6 Early Budding
plot.volcano(overlap.earlyBudding)
kable.overlap(overlap.earlyBudding)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 8.108032 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 6.004631 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 10.159023 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 5.040542 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0749261 | 8.068040 | 0.0000003 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr07g0311551 | 8.402186 | 0.0000003 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr10g0449721 | 8.187618 | 0.0000004 | (ATU2AF65B); (U2AF65B) | Putative U2A65 splicing factor which functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in shoot apex. Regulates flowering time and displays a redundant role in pollen tube growth together with AtU2AF65a. |
| HanXRQr2_Chr07g0311941 | 5.437609 | 0.0000008 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 5.437609 | 0.0000008 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr05g0230361 | 4.181710 | 0.0000022 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr06g0261551 | 5.090076 | 0.0000253 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr17g0793231 | 7.344466 | 0.0000363 | (AtCIB22);B22 SUBUNIT OF EUKARYOTIC MITOCHONDRIAL COMPLEX I (CIB22) | Encodes the B22 subunit of eukaryotic mitochondrial Complex I. Mutation in the gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr14g0626641 | 4.772837 | 0.0000425 | PUMILIO 1 (PUM1);PUMILIO 1 (APUM1) | Encodes a member of the Arabidopsis Pumilio (APUM) proteins containing PUF domain (eight repeats of approximately 36 amino acids each). PUF proteins regulate both mRNA stability and translation through sequence-specific binding to the 3’ UTR of target mRNA transcripts. |
| HanXRQr2_Chr13g0593361 | 4.304567 | 0.0001217 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr12g0533611 | -1.028211 | 0.0004457 | 0 | CDK inhibitor P21 binding protein;(source:Araport11) |
| HanXRQr2_Chr09g0362371 | 3.220069 | 0.0018403 | NA | NA |
| HanXRQr2_Chr01g0029451 | 1.424664 | 0.0019416 | HISTONE DEACETYLASE 9 (HDA9); (HDA09); (ATHDAC9);HISTONE DEACETYLASE 9 (HDAC9); (ATHDA9) | Encodes HDA9 (a RPD3-like histone deacetylase). Functions in promoting the onset of leaf senescence.The hda9 mutant shows enhanced H3K9 acetylation levels,based on immunodetection using H3K9ac antibodies. |
| HanXRQr2_Chr09g0380251 | -2.884747 | 0.0030317 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr04g0159131 | -2.093145 | 0.0034969 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0159711 | 4.802452 | 0.0044577 | EXPANSIN A1 (ATEXPA1);EXPANSIN 1 (EXP1);EXPANSIN A1 (EXPA1); (ATEXP1); (ATHEXP ALPHA 1.2); (AT-EXP1) | Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. |
| HanXRQr2_Chr04g0160711 | -4.203066 | 0.0046397 | GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (ASN1);ARABIDOPSIS THALIANA GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (AT-ASN1);DARK INDUCIBLE 6 (DIN6) | encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene’s expression pattern is responding to the level of sugar in the cell. |
| HanXRQr2_Chr04g0145031 | 1.898865 | 0.0080496 | SNF1-RELATED PROTEIN KINASE 3.24 (SnRK3.24);CBL-INTERACTING PROTEIN KINASE 5 (CIPK5) | Encodes CBL-interacting protein kinase 5 (CIPK5). |
| HanXRQr2_Chr08g0336101 | -5.360457 | 0.0110252 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160391 | -4.788130 | 0.0111159 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr08g0336081 | 2.053385 | 0.0118149 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr09g0372751 | -3.546616 | 0.0135798 | NA | Glycosyl hydrolase family 10 protein |
| HanXRQr2_Chr08g0337561 | -2.369916 | 0.0138988 | AGAMOUS-LIKE 3, AGL3, SEP4, SEPALLATA 4 | NA |
| HanXRQr2_Chr16g0763511 | 2.026421 | 0.0142503 | (ATSTE14); (STE14);HOMOLOG OF YEAST STE14 A (ATSTE14A);HOMOLOG OF YEAST STE14 A (STE14A);ARABIDOPSIS THALIANA ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ATICMTA);ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ICMTA);LPHA-CARBOXYL METHYLTRANSFERASE (ATPCM) | Encodes a prenylcysteine alpha-carboxyl methyltransferase involved in methylation of isoprenylated proteins. This protein appears to have lower catalytic activity and a lower transcript expression level than the other ICMT present in Arabidopsis (At5g08335). Analysis of ICMT RNAi lines suggests that this protein may be involved in flower and stem development. |
| HanXRQr2_Chr15g0711611 | -3.069025 | 0.0155622 | AGAMOUS-LIKE 4, AGL4, SEP2, SEPALLATA 2 | MADS-box protein, binds K domain of AG in vivo |
| HanXRQr2_Chr12g0552841 | -1.105022 | 0.0190930 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr09g0384381 | 3.559414 | 0.0227811 | 0 | transmembrane protein;(source:Araport11) |
| HanXRQr2_Chr10g0455551 | -1.351405 | 0.0268208 | ARABIDOPSIS THALIANA STARCH SYNTHASE 4 (ATSS4);STARCH SYNTHASE 4 (SS4);STARCH SYNTHASE 4 (SSIV) | Encodes a starch synthase. In Arabidopsis leaves, the catalytic C-terminal region of STARCH SYNTHASE 4 promotes starch granule initiation while its non-catalytic N-terminal region determines starch granules morphology. |
| HanXRQr2_Chr15g0692621 | 1.524295 | 0.0429592 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr12g0555521 | -1.812320 | 0.0486888 | ATRING1, RING1 | Encodes a RING finger domain protein with E3 ligase activity that is localized to the lipid rafts of the plasma membrane. Expression is increased in response to fungal pathogen. May be involved in regulation of programmed cell death by facilitating degredation of regulation of PDC activators. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr05g0230371 | 4.775595 | 0.0494866 | ARABIDOPSIS THALIANA RESPONSE REGULATOR 2 (ATRR2);RESPONSE REGULATOR 5 (RR5);INDUCED BY CYTOKININ 6 (IBC6);RESPONSE REGULATOR 5 (ARR5) | Encodes a transcription repressor that mediates a negative feedback loop in cytokinin signalling. ARR5 expression is upregulated by Class I KNOX genes. Arr5 protein is stabilized by cytokinin in a two-component phosphorelay. |
1.7 Late Budding
plot.volcano(overlap.lateBudding)
kable.overlap(overlap.lateBudding)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 8.042444 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 6.458279 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 10.186963 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 6.221948 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0749261 | 8.583986 | 0.0000001 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr07g0311551 | 8.679298 | 0.0000002 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr10g0449721 | 6.990209 | 0.0000022 | (ATU2AF65B); (U2AF65B) | Putative U2A65 splicing factor which functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in shoot apex. Regulates flowering time and displays a redundant role in pollen tube growth together with AtU2AF65a. |
| HanXRQr2_Chr07g0311941 | 4.728847 | 0.0000022 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 4.728847 | 0.0000022 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr02g0068731 | -3.973289 | 0.0000054 | 0 | Rhamnogalacturonate lyase family protein;(source:Araport11) |
| HanXRQr2_Chr06g0261551 | 5.580123 | 0.0000059 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr17g0793231 | 8.043046 | 0.0000106 | (AtCIB22);B22 SUBUNIT OF EUKARYOTIC MITOCHONDRIAL COMPLEX I (CIB22) | Encodes the B22 subunit of eukaryotic mitochondrial Complex I. Mutation in the gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0533611 | -1.221113 | 0.0000115 | 0 | CDK inhibitor P21 binding protein;(source:Araport11) |
| HanXRQr2_Chr15g0692621 | 3.214213 | 0.0000376 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr14g0650761 | -1.100581 | 0.0000476 | NA | Ribonuclease III family protein; FUNCTIONS IN: RNA binding, ribonuclease III activity; INVOLVED IN: RNA processing; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribonuclease III (InterPro:IPR000999); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT2G48121.2) |
| HanXRQr2_Chr04g0182161 | -1.295146 | 0.0000683 | NA | NA |
| HanXRQr2_Chr05g0230361 | 3.103737 | 0.0000874 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr04g0159131 | -2.541271 | 0.0000965 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr13g0593361 | 3.925409 | 0.0002022 | PHT5;3 | Encodes a member of the PHOSPHATE TRANSPORTER 5 family (PHT5;3). Overexpression of PHT5:3 leads to Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. |
| HanXRQr2_Chr09g0404641 | -4.235601 | 0.0004432 | HECATE 2 (HEC2) | Encodes a bHLH transcription factor that is involved in transmitting tract and stigma development. |
| HanXRQr2_Chr04g0160711 | -4.552573 | 0.0005279 | GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (ASN1);ARABIDOPSIS THALIANA GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (AT-ASN1);DARK INDUCIBLE 6 (DIN6) | encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene’s expression pattern is responding to the level of sugar in the cell. |
| HanXRQr2_Chr08g0337561 | -2.970068 | 0.0005676 | AGAMOUS-LIKE 3, AGL3, SEP4, SEPALLATA 4 | NA |
| HanXRQr2_Chr10g0423271 | 1.353936 | 0.0007200 | 0 | hypothetical protein (DUF506);(source:Araport11) |
| HanXRQr2_Chr12g0533581 | -1.588487 | 0.0007959 | CHLORORESPIRATORY REDUCTION 23 (CRR23);NADH DEHYDROGENASE-LIKE COMPLEX L (NdhL) | a subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in PSI cyclic electron transport. Located on the thylakoid membrane. Mutant has impaired NAD(P)H dehydrogenase activity. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0763511 | 2.716791 | 0.0008104 | (ATSTE14); (STE14);HOMOLOG OF YEAST STE14 A (ATSTE14A);HOMOLOG OF YEAST STE14 A (STE14A);ARABIDOPSIS THALIANA ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ATICMTA);ISOPRENYL CYSTEINE METHYLTRANSFERASE A (ICMTA);LPHA-CARBOXYL METHYLTRANSFERASE (ATPCM) | Encodes a prenylcysteine alpha-carboxyl methyltransferase involved in methylation of isoprenylated proteins. This protein appears to have lower catalytic activity and a lower transcript expression level than the other ICMT present in Arabidopsis (At5g08335). Analysis of ICMT RNAi lines suggests that this protein may be involved in flower and stem development. |
| HanXRQr2_Chr12g0552841 | -1.418573 | 0.0008255 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr09g0380251 | -2.861228 | 0.0009649 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr15g0706001 | 1.973741 | 0.0022007 | AGAMOUS-LIKE 22, AGL22, FAQ1, FLOWERING ARABIDOPSIS QTL1, SHORT VEGETATIVE PHASE, SVP | Encodes a nuclear protein that acts as a floral repressor and that functions within the thermosensory pathway. SVP represses FT expression via direct binding to the vCArG III motif in the FT promoter. |
| HanXRQr2_Chr10g0455551 | -1.655008 | 0.0022302 | ARABIDOPSIS THALIANA STARCH SYNTHASE 4 (ATSS4);STARCH SYNTHASE 4 (SS4);STARCH SYNTHASE 4 (SSIV) | Encodes a starch synthase. In Arabidopsis leaves, the catalytic C-terminal region of STARCH SYNTHASE 4 promotes starch granule initiation while its non-catalytic N-terminal region determines starch granules morphology. |
| HanXRQr2_Chr09g0362111 | -5.036336 | 0.0024189 | NA | NA |
| HanXRQr2_Chr10g0423911 | 3.194211 | 0.0028338 | AUTOINHIBITED CA(2+)-ATPASE, ISOFORM 4 (ACA4) | Encodes a calmodulin-regulated Ca(2+)-ATPase that improves salt tolerance in yeast. Localized to the vacuole. Lesion mimic phenotype when mutation in the gene is combined with a mutation in ACA11. Lesion mimic phenotype of double knockout can be suppressed by nutritional supplements that increase anion levels (e.g. 15 mM Nitrate, Chloride, or Phosphate). |
| HanXRQr2_Chr04g0181781 | -5.457789 | 0.0030582 | ARABIDOPSIS THALIANA P GLYCOPROTEIN1 (ATPGP1);ATP-BINDING CASSETTE B1 (ABCB1);P-GLYCOPROTEIN 1 (PGP1) | Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR1.Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AT3G28860. PGP1 mediates cellular efflux of IAA and interacts with PIN genes that may confer an accelerated vectoral component to PGP-mediated transport. The non-polar localization of PGP1 at root and shoot apices, where IAA gradient-driven transport is impaired, may be required to confer directionality to auxin transport in those tissues. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0409311 | 1.376932 | 0.0035211 | ARABIDOPSIS THALIANA HOMEOBOX 1, ATHB-1, ATHB1, CONSERVED PEPTIDE UPSTREAM OPEN READING FRAME 33, CPUORF33, HAT5, HB-1, HD-ZIP-1, HOMEOBOX 1, HOMEODOMAIN PROTEIN FROM ARABIDOIPSIS THALIANA 5 | Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf and hypocotyl development. Its promoter is bound by PIF1 which likely regulates its expression. Its translation is regulated by a conserved upstream ORF (CPuORF33) |
| HanXRQr2_Chr14g0626641 | 2.717264 | 0.0056820 | PUMILIO 1 (PUM1);PUMILIO 1 (APUM1) | Encodes a member of the Arabidopsis Pumilio (APUM) proteins containing PUF domain (eight repeats of approximately 36 amino acids each). PUF proteins regulate both mRNA stability and translation through sequence-specific binding to the 3’ UTR of target mRNA transcripts. |
| HanXRQr2_Chr06g0274391 | 1.715207 | 0.0056989 | CUTIN SYNTHASE2 (CUS2) | GDSL-motif esterase/acyltransferase/lipase. Enzyme group with broad substrate specificity that may catalyze acyltransfer or hydrolase reactions with lipid and non-lipid substrates. Mutants are defective in cuticle formation with reduced sepal cuticle ridge formation. |
| HanXRQr2_Chr04g0160391 | -5.000590 | 0.0063567 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr08g0336081 | 1.897515 | 0.0107872 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr04g0149371 | 3.077829 | 0.0119297 | CYTOCHROME P450, FAMILY 71, SUBFAMILY A, POLYPEPTIDE 22 (CYP71A22) | putative cytochrome P450 |
| HanXRQr2_Chr03g0090771 | 3.869407 | 0.0155186 | 6-PHOSPHOGLUCONOLACTONASE 3 (PGL3);EMBRYO DEFECTIVE 2024 (emb2024) | Encodes a protein with 6-phosphoglucunolactonase activity that localizes to the chloroplasts and the peroxisome. However, mutant phenotypes observed in pgl3 mutant plants can be complemented with a chloroplast-targeted version of the protein. PGL3 likely functions in the oxidative branch of the pentose phosphate pathway. pgl3 mutant phenotypes suggest that it is important in pathogen defense and maintenance of cellular redox homeostasis. |
| HanXRQr2_Chr09g0372751 | -2.923831 | 0.0161905 | NA | Glycosyl hydrolase family 10 protein |
| HanXRQr2_Chr05g0231181 | -1.462895 | 0.0174602 | ACHT4, ATYPICAL CYS HIS RICH THIOREDOXIN 4 | Encodes a member of the thioredoxin family protein. Located in the chloroplast. Shows high activity towards the chloroplast 2-Cys peroxiredoxin A, and poor activity towards the chloroplast NADP-malate dehydrogenase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0538051 | -2.298437 | 0.0209692 | SMALL AUXIN UPREGULATED RNA 52 (SAUR52) | SAUR-like auxin-responsive protein family;(source:Araport11) |
| HanXRQr2_Chr15g0711611 | -2.359784 | 0.0234752 | AGAMOUS-LIKE 4, AGL4, SEP2, SEPALLATA 2 | MADS-box protein, binds K domain of AG in vivo |
| HanXRQr2_Chr12g0547201 | 1.663561 | 0.0280758 | (BHLH49);CIB1 LIKE PROTEIN 1 (CIL1) | basic helix-loop-helix (bHLH) DNA-binding superfamily protein;(source:Araport11) |
| HanXRQr2_Chr08g0355341 | 6.030556 | 0.0284022 | (ATTPS21);TERPENE SYNTHASE 21 (TPS21) | Encodes a sesquiterpene synthase involved in generating all of the group A sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in the stigma. |
| HanXRQr2_Chr01g0022821 | -1.060232 | 0.0311641 | INHIBITOR/INTERACTOR WITH CYCLIN-DEPENDENT KINASE (ICK6) | Kip-related protein (KRP) gene, encodes CDK (cyclin-dependent kinase) inhibitor (CKI), negative regulator of cell division. Binds to D type and CDC2A cyclins and may inhibit cell cycle. Seven KRP genes were found in Arabidopsis thaliana. Differential expression patterns for distinct KRPs were revealed by in situ hybridization. |
| HanXRQr2_Chr09g0381361 | -1.576167 | 0.0346165 | ROTUNDIFOLIA LIKE 7 (RTFL7);DEVIL 8 (DVL8) | ROTUNDIFOLIA like 7;(source:Araport11) |
| HanXRQr2_Chr10g0447901 | 4.210121 | 0.0372096 | CRC, CRU3, CRUCIFERIN 3, CRUCIFERIN C | Encodes a 12S seed storage protein. The Landsberg erecta genome contains another copy of 12S globulin gene, CRA2, which is located tandemly with CRA1. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. |
| HanXRQr2_Chr09g0398411 | -1.631370 | 0.0404947 | 0 | membrane-associated kinase regulator-like protein;(source:Araport11) |
| HanXRQr2_Chr08g0342321 | -1.560296 | 0.0460523 | MAP KINASE KINASE 9 (MKK9); (ATMKK9) | member of MAP Kinase Kinase family. Autophosphorylates and also phosphorylates MPK3 and MPK6. Independently involved in ethylene and calmalexin biosynthesis. Induces transcription of ACS2, ACS6, ERF1, ERF2, ERF5, ERF6, CYP79B2, CYP79B3, CYP71A13 and PAD3. |
| HanXRQr2_Chr07g0303451 | 2.739755 | 0.0484980 | ATCRA1, CRA1, CRU1, CRUCIFERINA | Encodes a 12S seed storage protein. The Landsberg erecta genome contains another copy of 12S globulin gene, CRA2, which is located tandemly with CRA1. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. |
1.8 Endosperm
plot.volcano(overlap.endosperm)
kable.overlap(overlap.endosperm)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 7.669704 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 6.420030 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 8.734376 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | 5.792269 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr03g0099251 | -1.249158 | 0.0000000 | (MPK8); (ATMPK8) | Encodes mitogen-activated protein kinase 8 (MPK8). MPK8 connects protein phosphorylation, Ca2+, and ROS in the wound-signaling pathway. |
| HanXRQr2_Chr09g0381571 | 2.722904 | 0.0000016 | 0 | NAD(P)-binding Rossmann-fold superfamily protein;(source:Araport11) |
| HanXRQr2_Chr07g0311551 | 6.628103 | 0.0000028 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr07g0292791 | -4.370482 | 0.0000035 | CYTOCHROME P450, FAMILY 72, SUBFAMILY A, POLYPEPTIDE 15", CYP72A15 | putative cytochrome P450 The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr11g0520671 | -2.164675 | 0.0000051 | E-COAH-2, ECHIA, ENOYL-COA HYDRATASE 2, ENOYL-COA HYDRATASE/ISOMERASE A | enoyl-CoA hydratase/isomerase A (ECHIA); FUNCTIONS IN: catalytic activity; INVOLVED IN: metabolic process; LOCATED IN: peroxisome; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Crotonase, core (InterPro:IPR001753); BEST Arabidopsis thaliana protein match is: enoyl-CoA hydratase/isomerase D (TAIR:AT1G60550.1) |
| HanXRQr2_Chr05g0230361 | 3.886072 | 0.0000057 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr16g0749261 | 5.905106 | 0.0000058 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr04g0170431 | -1.096404 | 0.0000109 | CASEIN KINASE I-LIKE 6, CKL6, PAPK1 | casein kinase I-like 6 (CKL6); FUNCTIONS IN: protein serine/threonine kinase activity, kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasmodesma; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site (InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), Serine/threonine-protein kinase, active site (InterPro:IPR008271); BEST Arabidopsis thaliana protein match is: dual specificity kinase 1 (TAIR:AT1G03930.1) |
| HanXRQr2_Chr11g0475771 | -4.481695 | 0.0000116 | LYSM RLK1-INTERACTING KINASE 1 (LIK1) | Encodes LRR-RLK protein that is localized to the plasma membrane and is involved in regulation of plant innate immunity to microbes. LIK1 is phosphorylated by CERK1, a kinase involved in chitin perception. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0160711 | -8.279851 | 0.0000129 | GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (ASN1);ARABIDOPSIS THALIANA GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (AT-ASN1);DARK INDUCIBLE 6 (DIN6) | encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene’s expression pattern is responding to the level of sugar in the cell. |
| HanXRQr2_Chr07g0292811 | -3.465368 | 0.0000461 | NA | NA |
| HanXRQr2_Chr15g0692621 | -3.672169 | 0.0000591 | ATJMJ17, JMJ27, JMJC DOMAIN-CONTAINING PROTEIN 27 | Jumonji-domain-containing H3K9 histone demethylase. Loss of function mutants are susceptible to bacterial infection and early flowering. |
| HanXRQr2_Chr17g0793231 | 5.037286 | 0.0001034 | (AtCIB22);B22 SUBUNIT OF EUKARYOTIC MITOCHONDRIAL COMPLEX I (CIB22) | Encodes the B22 subunit of eukaryotic mitochondrial Complex I. Mutation in the gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr06g0261551 | 4.332894 | 0.0001352 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr14g0639041 | -2.531582 | 0.0001514 | ABS2 | AP2/B3-like transcriptional factor family protein |
| HanXRQr2_Chr14g0639131 | -1.051869 | 0.0002183 | MAG2 INTERACTING PROTEIN 1 (MIP1); (ATZW10) | Homologous to Drosophila ZW10, a centromere/kinetochore protein involved in chromosome segregation. Member of MAG2 complex on the ER that is responsible for efficient transport of seed storage proteins, functions in protein transport between the ER and Golgi apparatus, contain a Zeste?White 10 (ZW10) domain and a Sec39 domain. Required for proper maturation of seed storage proteins. |
| HanXRQr2_Chr09g0380251 | -3.683791 | 0.0002852 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr05g0231181 | -2.539110 | 0.0004670 | ACHT4, ATYPICAL CYS HIS RICH THIOREDOXIN 4 | Encodes a member of the thioredoxin family protein. Located in the chloroplast. Shows high activity towards the chloroplast 2-Cys peroxiredoxin A, and poor activity towards the chloroplast NADP-malate dehydrogenase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr10g0451771 | -1.228671 | 0.0004989 | NA | NA |
| HanXRQr2_Chr03g0098981 | 7.676744 | 0.0006027 | NA | Eukaryotic aspartyl protease family protein;(source:Araport11) |
| HanXRQr2_Chr03g0114791 | 1.285093 | 0.0006179 | EMBRYO DEFECTIVE 3120 (EMB3120) | hypothetical protein;(source:Araport11) |
| HanXRQr2_Chr08g0355111 | -3.679206 | 0.0026564 | KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 2 (KNAT2);ARABIDOPSIS THALIANA KN 1 (ATK1) | A member of class I knotted1-like homeobox gene family (together with KNAT1). Similar to the knotted1 (kn1) homeobox gene of maize. KNAT2 acts synergistically with cytokinins and antagonistically with ethylene based on ectopic expression studies in different mutant backgrounds and hormone treatments. In addition, KNAT2 is negatively regulated by AS and YABBY genes. KNAT2 is strongly expressed in the shoot apex of seedlings, while in mature plants the gene is primarily expressed in flowers and inflorescence stems. |
| HanXRQr2_Chr09g0405521 | 6.549279 | 0.0030623 | CLAVATA 1 (CLV1); (ATCLV1);FLOWER DEVELOPMENT 5 (FLO5);FASCIATA 3 (FAS3) | Putative receptor kinase with an extracellular leucine-rich domain. Controls shoot and floral meristem size, and contributes to establish and maintain floral meristem identity. Negatively regulated by KAPP (kinase-associated protein phosphatase). CLV3 peptide binds directly CLV1 ectodomain. |
| HanXRQr2_Chr10g0444291 | 1.232520 | 0.0034388 | DCT, DICARBOXYLATE TRANSPORT 2.1, DIT2.1 | dicarboxylate transport 2.1 |
| HanXRQr2_Chr08g0323061 | -1.069312 | 0.0046563 | ARABIDOPSIS PIN-FORMED 3 (ATPIN3);PIN-FORMED 3 (PIN3) | A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is expressed without pronounced polarity in tiers two and three of the columella cells, at the basal side of vascular cells, and to the lateral side of pericycle cells of the elongation zone. PIN3 overexpression inhibits root cell growth. Protein phosphorylation plays a role in regulating PIN3 trafficking tothe plasma membrane. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0556571 | -1.638604 | 0.0049173 | ZINC FINGER PROTEIN 4 (ZFP4) | Encodes a zinc finger protein containing only a single zinc finger. |
| HanXRQr2_Chr01g0013591 | 1.279717 | 0.0060193 | ATFAD2, FAD2, FATTY ACID DESATURASE 2 | Major enzyme responsible for the synthesis of 18:2 fatty acids in the endoplasmic reticulum. Contains His-rich motifs, which contribute to the interaction with the electron donor cytochrome b5. Mutations in this gene suppress the low temperature-induced phenotype of Arabidopsis tocopherol-deficient mutant vte2. |
| HanXRQr2_Chr11g0485451 | -6.092613 | 0.0061434 | UDP-GLUCOSYL TRANSFERASE 85A3 (AtUGT85A3);UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) | Encodes a putative UDP-glucosyl transferase. At1g22380 was initially identified as encoding the protein AAF87154, which has been classified as a bHLH protein (AtbHLH152). Subsequently it has been found that the AAF87154 protein appears to be encoded by the AT1G23970 genomic locus. |
| HanXRQr2_Chr09g0362111 | -6.904673 | 0.0063981 | NA | NA |
| HanXRQr2_Chr17g0807291 | -1.001620 | 0.0078020 | B-BOX DOMAIN PROTEIN 19, BBX19 | BBX19 is a B-box containing transcriptional regulator involved in photomporphogenesis and flowering. |
| HanXRQr2_Chr10g0423271 | 1.067988 | 0.0093408 | 0 | hypothetical protein (DUF506);(source:Araport11) |
| HanXRQr2_Chr06g0272711 | -3.422928 | 0.0094044 | UDP-GLUCOSYL TRANSFERASE 85A3 (AtUGT85A3);UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) | Encodes a putative UDP-glucosyl transferase. At1g22380 was initially identified as encoding the protein AAF87154, which has been classified as a bHLH protein (AtbHLH152). Subsequently it has been found that the AAF87154 protein appears to be encoded by the AT1G23970 genomic locus. |
| HanXRQr2_Chr11g0509401 | -7.766465 | 0.0103628 | ACH1, ATNRT2.1, ATNRT2:1, LATERAL ROOT INITIATION 1, LIN1, NITRATE TRANSPORTER 2, NITRATE TRANSPORTER 2.1, NITRATE TRANSPORTER 2:1, NRT2, NRT2.1, NRT2:1, NRT2;1AT | High-affinity nitrate transporter. Up-regulated by nitrate. Functions as a repressor of lateral root initiation independently of nitrate uptake. |
| HanXRQr2_Chr15g0708701 | -2.072681 | 0.0136469 | NITRATE REDUCTASE 2 (NIA2); (B29); (NIA2-1);ARABIDOPSIS NITRATE REDUCTASE 2 (ATNR2);NITRATE REDUCTASE (NR);NITRATE REDUCTASE 2 (NR2);CHLORATE RESISTANT 3 (CHL3) | Identified as a mutant resistant to chlorate. Encodes nitrate reductase structural gene. Involved in nitrate assimilation. Has nitrate reductase activity. Up-regulated by the fungus P. indica. Binds transcription factor At2g35940. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0533581 | -3.505846 | 0.0148232 | CHLORORESPIRATORY REDUCTION 23 (CRR23);NADH DEHYDROGENASE-LIKE COMPLEX L (NdhL) | a subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in PSI cyclic electron transport. Located on the thylakoid membrane. Mutant has impaired NAD(P)H dehydrogenase activity. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0731771 | -1.050077 | 0.0162415 | 0 | RING/U-box superfamily protein;(source:Araport11) |
| HanXRQr2_Chr05g0230371 | 3.989935 | 0.0162789 | ARABIDOPSIS THALIANA RESPONSE REGULATOR 2 (ATRR2);RESPONSE REGULATOR 5 (RR5);INDUCED BY CYTOKININ 6 (IBC6);RESPONSE REGULATOR 5 (ARR5) | Encodes a transcription repressor that mediates a negative feedback loop in cytokinin signalling. ARR5 expression is upregulated by Class I KNOX genes. Arr5 protein is stabilized by cytokinin in a two-component phosphorelay. |
| HanXRQr2_Chr15g0693421 | -6.198654 | 0.0163899 | (GH3-10);DWARF IN LIGHT 2 (DFL2) | Encodes a GH3-related gene involved in red light-specific hypocotyl elongation. Analysis of sense and antisense transgenic plants suggests that DFL2 is located downstream of red light signal transduction and determines the degree of hypocotyl elongation. |
| HanXRQr2_Chr09g0415631 | 1.479481 | 0.0209660 | DELTA TONOPLAST INTEGRAL PROTEIN (DELTA-TIP); (TIP2;1); (ATTIP2;1); (AQP1); (DELTA-TIP1) | Delta tonoplast intrinsic protein, functions as a water channel and ammonium (NH3) transporter. Highly expressed in flower, shoot, and stem. Expression shows diurnal regulation and is induced by ammonium (NH3). Protein localized to vacuolar membrane. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr14g0639781 | -1.093530 | 0.0215402 | GLUTAMATE DEHYDROGENASE 3 (GDH3) | GDH3 encodes a member of the glutamate dehydrogenease family. Its expression is upregulated in response to cytokinin and it may play a role in the control of nitrogen metabolism in leaf development. |
| HanXRQr2_Chr12g0552841 | -1.076748 | 0.0217965 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr15g0694721 | 1.474029 | 0.0241162 | 0 | Eukaryotic aspartyl protease family protein;(source:Araport11) |
| HanXRQr2_Chr05g0218451 | -3.182103 | 0.0254707 | ATMYB78, MYB DOMAIN PROTEIN 78, MYB78 | Member of the R2R3 factor gene family. |
| HanXRQr2_Chr04g0159081 | -3.566188 | 0.0278872 | UDP-GLUCOSYL TRANSFERASE 85A7 (UGT85A7);UDP-GLUCOSYL TRANSFERASE 85A7 (AtUGT85A7) | UDP-glucosyl transferase 85A7;(source:Araport11) |
| HanXRQr2_Chr10g0453001 | 1.350058 | 0.0285253 | “COLD, CIRCADIAN RHYTHM, AND RNA BINDING 2”, ATGRP7, CCR2, GLYCINE RICH PROTEIN 7, GLYCINE-RICH RNA-BINDING PROTEIN 7, GR-RBP7, GRP7, RBGA3, RNA-BINDING GLYCINE-RICH PROTEIN A3 | Encodes a small glycine-rich RNA binding protein that is part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript. Gene expression is induced by cold. GRP7 appears to promote stomatal opening and reduce tolerance under salt and dehydration stress conditions, but, promotes stomatal closing and thereby increases stress tolerance under conditions of cold tolerance. Loss of function mutations have increased susceptibility to pathogens suggesting a role in mediating innate immune response. Mutants are also late flowering in a non-photoperiodic manner and are responsive to vernalization suggesting an interaction with the autonomous flowering pathway. There is a reduction of mRNA export from the nucleus in grp7 mutants. GRP7:GFP fusion proteins can be found in the cytosol and nucleus. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase). |
| HanXRQr2_Chr10g0447901 | -2.089541 | 0.0343792 | CRC, CRU3, CRUCIFERIN 3, CRUCIFERIN C | Encodes a 12S seed storage protein. The Landsberg erecta genome contains another copy of 12S globulin gene, CRA2, which is located tandemly with CRA1. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. |
| HanXRQr2_Chr14g0626961 | 4.288957 | 0.0389077 | 0 | Ankyrin-repeat containing protein;(source:Araport11) |
| HanXRQr2_Chr12g0551271 | -3.468210 | 0.0413448 | (AtRHD6);ROOT HAIR DEFECTIVE6 (RHD6) | ROOT HAIR DEFECTIVE6;(source:Araport11) |
| HanXRQr2_Chr15g0698701 | -1.353183 | 0.0416420 | NA | Dof-type zinc finger DNA-binding family protein;(source:Araport11) |
| HanXRQr2_Chr07g0309641 | 2.245952 | 0.0458514 | AGAMOUS-LIKE 8, AGL8, FRUITFULL, FUL | MADS box gene negatively regulated by APETALA1 |
| HanXRQr2_Chr09g0372751 | -2.733078 | 0.0469223 | NA | Glycosyl hydrolase family 10 protein |
1.9 Seedcoat
plot.volcano(overlap.seedcoat)
kable.overlap(overlap.seedcoat)| gene | logFC | FDR | gene name | gene description |
|---|---|---|---|---|
| HanXRQr2_Chr13g0578191 | 6.561643 | 0.0000000 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 7.218647 | 0.0000000 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr09g0384341 | -9.060557 | 0.0000000 | UDP-GLUCOSYL TRANSFERASE 88A1 (UGT88A1) | UDP-glucosyl transferase 88A1;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 7.410956 | 0.0000000 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr09g0371441 | 5.463129 | 0.0000000 | CAFFEOYL COENZYME A ESTER O-METHYLTRANSFERASE 7, CCOAOMT7 | Encodes a caffeoyl-coenzyme A O-methyltransferase (CCoAOMT)-like protein with a strong preference for methylating the para position of flavanones and dihydroflavonols, whereas flavones and flavonols are methylated in the meta-position. |
| HanXRQr2_Chr04g0160001 | 5.361749 | 0.0000000 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr01g0013591 | -3.998420 | 0.0000000 | ATFAD2, FAD2, FATTY ACID DESATURASE 2 | Major enzyme responsible for the synthesis of 18:2 fatty acids in the endoplasmic reticulum. Contains His-rich motifs, which contribute to the interaction with the electron donor cytochrome b5. Mutations in this gene suppress the low temperature-induced phenotype of Arabidopsis tocopherol-deficient mutant vte2. |
| HanXRQr2_Chr13g0593301 | -7.837832 | 0.0000000 | (WES1); (GH3.5) | encodes an IAA-amido synthase that conjugates Asp and other amino acids to auxin in vitro. Lines carrying insertions in this gene are hypersensitive to auxin. It is involved in camalexin biosynthesis via conjugating indole-3-carboxylic acid (ICA) and cysteine (Cys). The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0158821 | 1.995604 | 0.0000000 | HISTIDINE-CONTAINING PHOSPHOTRANSFER FACTOR 5 (AHP5) | Encodes AHP5, one of the six Arabidopsis thaliana histidine phosphotransfer proteins (AHPs). AHPs function as redundant positive regulators of cytokinin signaling. Members of the AHP gene family include: AT3G21510 (AHP1), AT3G29350 (AHP2), AT5G39340 (AHP3), AT3G16360 (AHP4), AT1G03430 (AHP5) and AT1G80100 (AHP6). |
| HanXRQr2_Chr09g0415631 | 4.296688 | 0.0000000 | DELTA TONOPLAST INTEGRAL PROTEIN (DELTA-TIP); (TIP2;1); (ATTIP2;1); (AQP1); (DELTA-TIP1) | Delta tonoplast intrinsic protein, functions as a water channel and ammonium (NH3) transporter. Highly expressed in flower, shoot, and stem. Expression shows diurnal regulation and is induced by ammonium (NH3). Protein localized to vacuolar membrane. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr05g0230361 | 4.919156 | 0.0000001 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr14g0670291 | -1.525507 | 0.0000002 | PKP3, PLASTIDIAL PYRUVATE KINASE 3 | encodes a chloroplast pyruvate kinase beta subunit. The enzyme is less active than the other chloroplast pyruvate kinase beta subunit encoded by AT5G52920. Involved in seed oil biosynthesis. Can partially complement the AT5G52920 mutant. |
| HanXRQr2_Chr07g0311551 | 7.053604 | 0.0000003 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr12g0551571 | -1.594524 | 0.0000006 | IAA8, INDOLEACETIC ACID-INDUCED PROTEIN 8 | Encodes a transcriptional repressor of the auxin response that is auxin inducible and is involved in lateral root formation. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0416891 | -2.698768 | 0.0000008 | 0 | Protein kinase superfamily protein;(source:Araport11) |
| HanXRQr2_Chr09g0379931 | -2.642642 | 0.0000015 | (PLA IIB);PATATIN-LIKE PROTEIN 6 (PLP6) | PATATIN-like protein 6;(source:Araport11) |
| HanXRQr2_Chr05g0216981 | 2.523230 | 0.0000018 | 0 | Pyruvate kinase family protein;(source:Araport11) |
| HanXRQr2_Chr17g0801201 | 5.908034 | 0.0000021 | (AZI5) | Encodes a member of the AZI family of lipid transfer proteins. |
| HanXRQr2_Chr13g0578271 | -1.215236 | 0.0000021 | (SCL6-IV);LOST MERISTEMS 3 (LOM3);ARABIDOPSIS THALIANA HAIRY MERISTEM 3 (ATHAM3);HAIRY MERISTEM 3 (HAM3) | Belongs to one of the LOM (LOST MERISTEMS) genes: AT2G45160 (LOM1), AT3G60630 (LOM2) and AT4G00150 (LOM3). LOM1 and LOM2 promote cell differentiation at the periphery of shoot meristems and help to maintain their polar organization. |
| HanXRQr2_Chr03g0094331 | 6.979614 | 0.0000021 | IBH1-LIKE 1 (IBL1) | sequence-specific DNA binding transcription factor;(source:Araport11) |
| HanXRQr2_Chr15g0708701 | 5.064061 | 0.0000024 | NITRATE REDUCTASE 2 (NIA2); (B29); (NIA2-1);ARABIDOPSIS NITRATE REDUCTASE 2 (ATNR2);NITRATE REDUCTASE (NR);NITRATE REDUCTASE 2 (NR2);CHLORATE RESISTANT 3 (CHL3) | Identified as a mutant resistant to chlorate. Encodes nitrate reductase structural gene. Involved in nitrate assimilation. Has nitrate reductase activity. Up-regulated by the fungus P. indica. Binds transcription factor At2g35940. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0170431 | -1.155730 | 0.0000025 | CASEIN KINASE I-LIKE 6, CKL6, PAPK1 | casein kinase I-like 6 (CKL6); FUNCTIONS IN: protein serine/threonine kinase activity, kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasmodesma; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site (InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), Serine/threonine-protein kinase, active site (InterPro:IPR008271); BEST Arabidopsis thaliana protein match is: dual specificity kinase 1 (TAIR:AT1G03930.1) |
| HanXRQr2_Chr14g0656381 | 4.496804 | 0.0000028 | ATMYB38, BIT1, BLUE INSENSITIVE TRAIT 1, MYB DOMAIN PROTEIN 38, MYB38, RAX2, REGULATOR OF AXILLARY MERISTEMS 2 | “Putative homolog of the Blind gene in tomato. Together with RAX1 and RAX3 belong to the class R2R3 MYB genes; encoded by the Myb-like transcription factor MYB38, regulates axillary meristem formation.” The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr13g0571341 | -3.314008 | 0.0000029 | FAD2-3!!! ATFAD2, FAD2, FATTY ACID DESATURASE 2 | Major enzyme responsible for the synthesis of 18:2 fatty acids in the endoplasmic reticulum. Contains His-rich motifs, which contribute to the interaction with the electron donor cytochrome b5. Mutations in this gene suppress the low temperature-induced phenotype of Arabidopsis tocopherol-deficient mutant vte2. |
| HanXRQr2_Chr16g0744931 | 3.869048 | 0.0000030 | ARABIDOPSIS THALIANA TONOPLAST INTRINSIC PROTEIN 2;3 (ATTIP2;3);TONOPLAST INTRINSIC PROTEIN 2;3 (TIP2;3);DELTA-TONOPLAST INTRINSIC PROTEIN 3 (DELTA-TIP3) | Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3). |
| HanXRQr2_Chr10g0442521 | -3.283008 | 0.0000045 | (B120) | S-locus lectin protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr11g0485121 | 1.193158 | 0.0000048 | CN, CONVOLUTA, SPIRAL 2, SPR2, TOR1, TORTIFOLIA 1 | NA |
| HanXRQr2_Chr01g0032931 | -1.185115 | 0.0000067 | EMB1011, EMBRYO DEFECTIVE 1011, LNO1, LONO 1 | Nuclear pore complex protein |
| HanXRQr2_Chr06g0261551 | 5.295638 | 0.0000081 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr13g0579691 | -2.078918 | 0.0000102 | GATA TRANSCRIPTION FACTOR 15 (GATA15) | Encodes a member of the GATA factor family of zinc finger transcription factors. |
| HanXRQr2_Chr12g0549501 | -1.030721 | 0.0000121 | NA | NA |
| HanXRQr2_Chr08g0323061 | -2.046754 | 0.0000175 | ARABIDOPSIS PIN-FORMED 3 (ATPIN3);PIN-FORMED 3 (PIN3) | A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is expressed without pronounced polarity in tiers two and three of the columella cells, at the basal side of vascular cells, and to the lateral side of pericycle cells of the elongation zone. PIN3 overexpression inhibits root cell growth. Protein phosphorylation plays a role in regulating PIN3 trafficking tothe plasma membrane. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr16g0749261 | 4.809281 | 0.0000219 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr14g0639781 | -2.079182 | 0.0000258 | GLUTAMATE DEHYDROGENASE 3 (GDH3) | GDH3 encodes a member of the glutamate dehydrogenease family. Its expression is upregulated in response to cytokinin and it may play a role in the control of nitrogen metabolism in leaf development. |
| HanXRQr2_Chr12g0538051 | 4.421325 | 0.0000278 | SMALL AUXIN UPREGULATED RNA 52 (SAUR52) | SAUR-like auxin-responsive protein family;(source:Araport11) |
| HanXRQr2_Chr15g0690651 | -6.485388 | 0.0000420 | “CYTOCHROME P450, FAMILY 71, SUBFAMILY A, POLYPEPTIDE 23”, CYP71A23 | putative cytochrome P450 |
| HanXRQr2_Chr12g0552511 | -1.906409 | 0.0000522 | ATMYB73, MYB DOMAIN PROTEIN 73, MYB73 | Member of the R2R3 factor gene family. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr12g0551621 | -1.162491 | 0.0000682 | NA | UDP-Glycosyltransferase superfamily protein |
| HanXRQr2_Chr14g0639131 | -1.086489 | 0.0000818 | MAG2 INTERACTING PROTEIN 1 (MIP1); (ATZW10) | Homologous to Drosophila ZW10, a centromere/kinetochore protein involved in chromosome segregation. Member of MAG2 complex on the ER that is responsible for efficient transport of seed storage proteins, functions in protein transport between the ER and Golgi apparatus, contain a Zeste?White 10 (ZW10) domain and a Sec39 domain. Required for proper maturation of seed storage proteins. |
| HanXRQr2_Chr06g0251521 | 1.077933 | 0.0000955 | ATEBP, EBP, ERF72, ETHYLENE RESPONSE FACTOR 72, ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN, RAP2.3, RELATED TO AP2 3 | Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr03g0127741 | -2.689868 | 0.0001013 | BETA-KETOACYL-ACP SYNTHETASE 2 (KAS2);FATTY ACID BIOSYNTHESIS 1 (FAB1) | Encodes a plastidic beta-ketoacyl-ACP synthase II, involved in fatty acid elongation from 16:0-ACP to 18:0-ACP. Homozygous knock-out mutants are embryo lethal, indicating early embryo development is sensitive to elevated 16:0. |
| HanXRQr2_Chr13g0607011 | -1.466065 | 0.0001067 | HOMEOBOX PROTEIN 2 (ATHB-2);HOMEOBOX PROTEIN 2 (HB-2);ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2 (ATHB2); (HAT4) | Encodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr15g0711571 | 2.346586 | 0.0001075 | LONGIFOLIA1 (LNG1); (ATLNG1);TON1 RECRUITING MOTIF 2 (TRM2) | Encodes LONGIFOLIA1 (LNG1). Regulates leaf morphology by promoting cell expansion in the leaf-length direction. The LNG1 homologue LNG2 (At3g02170) has similar function. |
| HanXRQr2_Chr04g0160711 | -6.065539 | 0.0001257 | GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (ASN1);ARABIDOPSIS THALIANA GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1 (AT-ASN1);DARK INDUCIBLE 6 (DIN6) | encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene’s expression pattern is responding to the level of sugar in the cell. |
| HanXRQr2_Chr15g0698841 | 1.762214 | 0.0001294 | (AtTIR1);TRANSPORT INHIBITOR RESPONSE 1 (TIR1) | Encodes an auxin receptor that mediates auxin-regulated transcription.It contains leucine-rich repeats and an F-box and interacts with ASK1, ASK2 and AtCUL1 to form SCF-TIR1, an SCF ubiquitin ligase complex. Related to yeast Grr1p and human SKP2 proteins, involved in ubiquitin-mediated processes. Required for normal response to auxin and repressed in response to flagellin.As part of the SCF complex and in the presence of auxin, TIR1 interacts with Aux/IAA transcriptional repressor proteins and mediates their degradation. Mutations in TIR1 block auxin stimulation of flavonoid synthesis. |
| HanXRQr2_Chr16g0744861 | 1.267462 | 0.0001305 | APRR2, PRR2, PSEUDO-RESPONSE REGULATOR 2 | Encodes pseudo-response regulator 2 (APRR2) that interacts with a calcium sensor (CML9). |
| HanXRQr2_Chr09g0380251 | -3.622126 | 0.0001428 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
| HanXRQr2_Chr15g0679121 | -6.336886 | 0.0001482 | CYSTEINE PROTEINASE INHIBITOR 5 (CYS5) | Putative phytocystatin expressed in seedlings and induced by heat stress and abscisic acid. Overexpression increases germination rate and heat stress tolerance. CYS5 is a target of ABF1 and ABF3 transcriptional regulators which bind to its promoter. |
| HanXRQr2_Chr16g0735881 | 1.315286 | 0.0001657 | NA | tRNA-processing ribonuclease BN;(source:Araport11) |
| HanXRQr2_Chr08g0351521 | -1.319416 | 0.0001789 | CN, CONVOLUTA, SPIRAL 2, SPR2, TOR1, TORTIFOLIA 1 | Encodes a novel, plant-specific microtubule-associated protein that regulates the orientation of cortical microtubules and the direction of organ growth. The protein plays a role in control of microtubule dependent anisotropic cell elongation. spr2 mutant rosette leaves, cauline leaves, roots, petioles and petals curl in an anticlockwise direction. |
| HanXRQr2_Chr13g0593351 | -3.516994 | 0.0001878 | ORGANIC CATION/CARNITINE TRANSPORTER4 (AtOCT4);ORGANIC CATION/CARNITINE TRANSPORTER4 (OCT4) | organic cation/carnitine transporter4;(source:Araport11) |
| HanXRQr2_Chr03g0127771 | -4.073276 | 0.0002447 | DMR6-LIKE OXYGENASE 2 (DLO2) | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein;(source:Araport11) |
| HanXRQr2_Chr02g0066401 | 1.899326 | 0.0003188 | OBF4, OCS ELEMENT BINDING FACTOR 4, TGA4, TGACG MOTIF-BINDING FACTOR 4 | Encodes a member of basic leucine zipper transcription gene family. Nomenclature according to Xiang, et al. (1997). |
| HanXRQr2_Chr08g0359491 | -5.205869 | 0.0003194 | MYB DOMAIN PROTEIN 108 (MYB108);BOTRYTIS-SUSCEPTIBLE1 (BOS1);MYB DOMAIN PROTEIN 108 (AtMYB108) | putative transcription factor MYB108 (MYB108) mRNA, |
| HanXRQr2_Chr06g0274391 | -3.243816 | 0.0003331 | CUTIN SYNTHASE2 (CUS2) | GDSL-motif esterase/acyltransferase/lipase. Enzyme group with broad substrate specificity that may catalyze acyltransfer or hydrolase reactions with lipid and non-lipid substrates. Mutants are defective in cuticle formation with reduced sepal cuticle ridge formation. |
| HanXRQr2_Chr07g0311941 | 3.103545 | 0.0003333 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr07g0311941 | 3.103545 | 0.0003333 | 0 | Leucine-rich repeat protein kinase family protein;(source:Araport11) |
| HanXRQr2_Chr11g0474921 | -3.781289 | 0.0003367 | ARABIDOPSIS THALIANA GIBBERELLIN 2-OXIDASE 1, ATGA2OX1, GA2OX1, GIBBERELLIN 2-OXIDASE 1 | Encodes a gibberellin 2-oxidase that acts on C19 gibberellins. |
| HanXRQr2_Chr06g0274231 | 4.993641 | 0.0003724 | REDUCED STEM BRANCHING 8 (RSB8);FLOWERING LOCUS T (FT) | FT, together with LFY, promotes flowering and is antagonistic with its homologous gene, TERMINAL FLOWER1 (TFL1). Together with TSF, it plays an antagonistic role to TFL1 in the determination of inflorescence meristem identity. FT is expressed in leaves and is induced by long day treatment. Either the FT mRNA or protein is translocated to the shoot apex where it induces its own expression. Recent data suggests that FT protein acts as a long-range signal. FT is a target of CO and acts upstream of SOC1. |
| HanXRQr2_Chr04g0145031 | 2.229585 | 0.0004564 | SNF1-RELATED PROTEIN KINASE 3.24 (SnRK3.24);CBL-INTERACTING PROTEIN KINASE 5 (CIPK5) | Encodes CBL-interacting protein kinase 5 (CIPK5). |
| HanXRQr2_Chr08g0336101 | -6.602586 | 0.0004978 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr08g0336081 | 2.671222 | 0.0005542 | 0 | disease resistance family protein / LRR family protein;(source:Araport11) |
| HanXRQr2_Chr14g0644441 | -1.213421 | 0.0006131 | PAS2, PASTICCINO 2, PEP, PEPINO | Protein tyrosine phosphatase-like involved in cell division and differentiation. Interacts with CDKA;1 only in its phosphorylated form, preventing dephosphorylation. Overexpression slowed down cell division in suspension cell cultures at the G2-to-M transition and early mitosis and inhibited Arabidopsis seedling growth. Localized in the cytoplasm of dividing cells but moved into the nucleus upon cell differentiation. Based on complementation of yeast mutant PAS2 has acyl-CoA dehydratase activity. It interacts with CER10, a component of the microsomal fatty acid elongase complex, suggesting a role in synthesis of VLCFAs (very long chain fatty acids). |
| HanXRQr2_Chr04g0174741 | -2.167902 | 0.0006171 | XBCP3, XYLEM BARK CYSTEINE PEPTIDASE 3 | Arabidopsis thaliana papain-like cysteine peptidase |
| HanXRQr2_Chr04g0159521 | 1.130528 | 0.0008051 | AUXIN SIGNALING F-BOX 4 (AFB4) | RNI-like superfamily protein;(source:Araport11) |
| HanXRQr2_Chr09g0362371 | -3.551018 | 0.0008199 | NA | NA |
| HanXRQr2_Chr07g0285021 | -1.298538 | 0.0008273 | NAC DOMAIN CONTAINING PROTEIN 103 (anac103);NAC DOMAIN CONTAINING PROTEIN 103 (NAC103) | NAC domain containing protein 103;(source:Araport11) |
| HanXRQr2_Chr01g0025561 | -4.230731 | 0.0008857 | FATTY ACID EXPORT 1, FAX1 | Encodes a chloroplast inner envelope localized member of the Tmemb_14 gene family. FAX1 is involved in fatty acid and lipid homeostasis and likely functions as a fatty acid transporter that exports fatty acids from the plastid. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr05g0218451 | -4.975919 | 0.0014539 | ATMYB78, MYB DOMAIN PROTEIN 78, MYB78 | Member of the R2R3 factor gene family. |
| HanXRQr2_Chr14g0639041 | -1.927742 | 0.0015504 | ABS2 | AP2/B3-like transcriptional factor family protein |
| HanXRQr2_Chr15g0711611 | -3.695783 | 0.0016584 | AGAMOUS-LIKE 4, AGL4, SEP2, SEPALLATA 2 | MADS-box protein, binds K domain of AG in vivo |
| HanXRQr2_Chr15g0698701 | 1.807309 | 0.0017562 | NA | Dof-type zinc finger DNA-binding family protein;(source:Araport11) |
| HanXRQr2_Chr09g0415751 | 2.024513 | 0.0018044 | GATA TRANSCRIPTION FACTOR 12 (GATA12) | Encodes a member of the GATA factor family of zinc finger transcription factors. |
| HanXRQr2_Chr15g0689291 | 2.546970 | 0.0018077 | GLABROUS INFLORESCENCE STEMS 3 (GIS3) | Encodes a nuclear localized member of the C2H2 family of TFIIIA transcription factors.GIS3 is involved in trichome initiation and development downstream of GA and cytokinin signaling. GIS regulates the expression GIS and GIS2. |
| HanXRQr2_Chr12g0552841 | -1.400716 | 0.0018502 | 0 | Sec14p-like phosphatidylinositol transfer family protein;(source:Araport11) |
| HanXRQr2_Chr11g0509931 | 3.524014 | 0.0020147 | MEDOS 2 (MDS2) | Involved in growth adaptation upon exposure to metal ions. Contributes together with the other MDS genes to the complex network of CrRLK1Ls that positively and negatively affect growth. |
| HanXRQr2_Chr13g0609081 | 2.262440 | 0.0021777 | LATERAL ROOT PRIMORDIUM 1 (LRP1) | A member of SHI gene family. Arabidopsis thaliana has ten members that encode proteins with a RING finger-like zinc finger motif. Despite being highly divergent in sequence, many of the SHI-related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis. Expressed in lateral root primordia and induced by auxin. SWP1 is involved in the repression of LRP1 via histone deacetylation. |
| HanXRQr2_Chr09g0409291 | 2.894072 | 0.0024906 | ABA-IMPORTING TRANSPORTER 1, AIT1, ATNPF4.6, ATNRT1:2, NITRATE TRANSPORTER 1:2, NPF4.6, NRT1.2, NRT1/ PTR FAMILY 4.6, NRT1:2, NTL1 | Encodes an inducible component of low-affinity nitrate uptake. mRNA found primarily in root hairs and the epidermis of roots. It also acts as an ABA importer at the site of ABA biosynthesis and is important for the regulation of stomatal aperture in inflorescence stems. |
| HanXRQr2_Chr04g0174371 | -3.840443 | 0.0026614 | TREHALOSE-PHOSPHATASE/SYNTHASE 7 (ATTPS7);TREHALOSE-PHOSPHATASE/SYNTHASE 7 (TPS7); (ATTPSA);TREHALOSE -6-PHOSPHATASE SYNTHASE S7 (TPS7) | Encodes an enzyme putatively involved in trehalose biosynthesis. Though the protein has both trehalose-6-phosphate synthase (TPS)-like and trehalose-6-phosphate phosphatase (TPP)-like domains, neither activity has been detected in enzymatic assays nor has the protein been able to complement yeast TPS or TPP mutants. |
| HanXRQr2_Chr11g0485111 | 1.369378 | 0.0026631 | 0 | hexon;(source:Araport11) |
| HanXRQr2_Chr08g0334381 | -1.528130 | 0.0029983 | ARF1-BINDING PROTEIN, ARF1-BP, ARF2, ATARF2, AUXIN RESPONSE FACTOR 2, HLS1 SUPPRESSOR, HSS, ORE14, ORESARA 14 | Encodes an auxin response factor. Mutants have many defects including enlarged rosette leaves, reduced fertility, later senescence, hypocotyl elongation defects, enlarged seeds and enlarged cotyledons. May not mediate auxin effects. Increase in seed size due to increased cell proliferation. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr13g0579711 | -1.080997 | 0.0032184 | RESPONSE REGULATOR 1 (RR1);RESPONSE REGULATOR 1 (ARR1) | Encodes an Arabidopsis response regulator (ARR) protein that acts in concert with other type-B ARRs in the cytokinin signaling pathway. Also involved in cytokinin-dependent inhibition of hypocotyl elongation and cytokinin-dependent greening and shooting in tissue culture. ARR1, ARR10, and ARR12 are redundant regulators of drought response, with ARR1 being the most critical. ARR1, ARR10 and ARR12 redundantly bind to the promoter of WUSCHEL (WUS), directly activate its transcription. In parallel, ARR1, ARR10 and ARR12 repress the expression of YUCCAs (YUCs), which encode a key enzyme for auxin biosynthesis, indirectly promoting WUS induction. The regulation of ARR1, ARR10 and ARR12 on WUS and YUCs is required for regeneration and maintenance of shoot meristem. |
| HanXRQr2_Chr13g0600351 | -6.430990 | 0.0035379 | 0 | Encodes for a 4-coumarate-CoA ligase involved in the biosynthesis of the benzenoid ring of ubiquinone from phenylalanine. |
| HanXRQr2_Chr13g0596441 | -1.173663 | 0.0035416 | ATCBL10, CALCINEURIN B-LIKE PROTEIN 10, CBL10, SCABP8, SOS3-LIKE CALCIUM BINDING PROTEIN 8 | Encodes a member of the calcineurin B-like calcium sensor gene family. Mediates salt tolerance by regulating ion homeostasis in Arabidopsis. |
| HanXRQr2_Chr09g0362111 | 5.157163 | 0.0035693 | NA | NA |
| HanXRQr2_Chr08g0358361 | -1.229350 | 0.0036521 | AGAMOUS-LIKE 104 (AGL104) | Encodes a member of the MIKC (MADS box, Keratin binding domain, and C terminal domain containing )family of transcriptional regulators. AGL104 is expressed in pollen.It forms heterodimers with other MICK family members (AGL65 and AGL30). Involved in late stages of pollen development and pollen tube growth. |
| HanXRQr2_Chr14g0626641 | 2.770773 | 0.0036842 | PUMILIO 1 (PUM1);PUMILIO 1 (APUM1) | Encodes a member of the Arabidopsis Pumilio (APUM) proteins containing PUF domain (eight repeats of approximately 36 amino acids each). PUF proteins regulate both mRNA stability and translation through sequence-specific binding to the 3’ UTR of target mRNA transcripts. |
| HanXRQr2_Chr04g0158921 | 1.513881 | 0.0038358 | BETA-XYLOSIDASE 2 (ATBXL2);BETA-XYLOSIDASE 2 (BXL2) | encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members. |
| HanXRQr2_Chr09g0415601 | -2.058470 | 0.0040200 | INDOLE-3-ACETIC ACID INDUCIBLE 27 (IAA27);PHYTOCHROME-ASSOCIATED PROTEIN 2 (PAP2) | phytochrome-associated protein 2 (PAP2) |
| HanXRQr2_Chr07g0292811 | 1.864822 | 0.0042418 | NA | NA |
| HanXRQr2_Chr04g0160801 | -1.135048 | 0.0043913 | TANDEM ZINC FINGER PROTEIN 9 (TZF9) | zinc finger (CCCH-type) family protein;(source:Araport11) |
| HanXRQr2_Chr07g0292331 | -2.004953 | 0.0045677 | AGAMOUS-LIKE 22, AGL22, FAQ1, FLOWERING ARABIDOPSIS QTL1, SHORT VEGETATIVE PHASE, SVP | Encodes a nuclear protein that acts as a floral repressor and that functions within the thermosensory pathway. SVP represses FT expression via direct binding to the vCArG III motif in the FT promoter. |
| HanXRQr2_Chr09g0396651 | 2.381179 | 0.0049196 | KARRIKIN INSENSITIVE 2 (KAI2) | HTL belonging to the alpha/beta fold hydrolase superfamily. Mutant and over-expression studies indicates its involvement in seedling de-etiolation process. |
| HanXRQr2_Chr09g0390591 | -1.018939 | 0.0098181 | SUPPRESSOR OF QUENCHING 1 (SOQ1) | Encodes a thylakoid membrane protein with thioredoxin-like and beta-propeller domains located in the lumen and a haloacid-dehalogenase domain exposed to the chloroplast stroma. The protein’s role may be to prevent formation of a slowly reversible form of antenna quenching, thereby maintaining the efficiency of light harvesting. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr09g0381361 | 3.734358 | 0.0105286 | ROTUNDIFOLIA LIKE 7 (RTFL7);DEVIL 8 (DVL8) | ROTUNDIFOLIA like 7;(source:Araport11) |
| HanXRQr2_Chr04g0159081 | -5.133810 | 0.0116790 | UDP-GLUCOSYL TRANSFERASE 85A7 (UGT85A7);UDP-GLUCOSYL TRANSFERASE 85A7 (AtUGT85A7) | UDP-glucosyl transferase 85A7;(source:Araport11) |
| HanXRQr2_Chr11g0492511 | 1.159986 | 0.0122354 | DIVARICATA1 (DIV1) | R-R-type MYB protein |
| HanXRQr2_Chr15g0702591 | -3.578616 | 0.0135276 | EMB2473, EMBRYO DEFECTIVE 2473, MIRO-RELATED GTP-ASE 1, MIRO1 | NA |
| HanXRQr2_Chr11g0475771 | -3.617219 | 0.0137156 | LYSM RLK1-INTERACTING KINASE 1 (LIK1) | Encodes LRR-RLK protein that is localized to the plasma membrane and is involved in regulation of plant innate immunity to microbes. LIK1 is phosphorylated by CERK1, a kinase involved in chitin perception. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0160171 | 2.055144 | 0.0138600 | XYLOGLUCAN ENDOTRANSGLYCOSYLASE RELATED 2 (XTR2);XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 28 (XTH28); (ATXTH28);ENDOXYLOGLUCAN TRANSFERASE A2 (EXGT-A2) | member of Glycoside Hydrolase Family 16 |
| HanXRQr2_Chr04g0159131 | 1.690547 | 0.0148080 | GENERAL REGULATORY FACTOR 2 (GRF2);14-3-3 PROTEIN G-BOX FACTOR14 OMEGA (14-3-3OMEGA); (GF14 OMEGA) | G-box binding factor GF14 omega encoding a 14-3-3 protein The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr04g0161431 | -3.857399 | 0.0176785 | ATMYB59, ATMYB59-1, ATMYB59-2, ATMYB59-3, MYB DOMAIN PROTEIN 59, MYB59 | Encodes a putative transcription factor (MYB59). |
| HanXRQr2_Chr03g0090771 | -3.851729 | 0.0186571 | 6-PHOSPHOGLUCONOLACTONASE 3 (PGL3);EMBRYO DEFECTIVE 2024 (emb2024) | Encodes a protein with 6-phosphoglucunolactonase activity that localizes to the chloroplasts and the peroxisome. However, mutant phenotypes observed in pgl3 mutant plants can be complemented with a chloroplast-targeted version of the protein. PGL3 likely functions in the oxidative branch of the pentose phosphate pathway. pgl3 mutant phenotypes suggest that it is important in pathogen defense and maintenance of cellular redox homeostasis. |
| HanXRQr2_Chr04g0174691 | 7.100615 | 0.0210242 | ATGPAT9, GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 9, GPAT9 | lycerol-3-phosphate acyltransferase localized to the ER. Similar to mammalian cells involved in storage oil formation. ER-localized GPAT enzyme responsible for plant membrane lipid and oil biosynthesis |
| HanXRQr2_Chr03g0127681 | -1.626223 | 0.0220773 | (NUP98A);DRACULA2 (DRA2) | DRA2 is a homolog of mammalian nucleoporin 98 and a likely component of the nuclear pore complex in Arabidopsis. It positively participates in the control of the hypocotyl elongation response to plant proximity and control of shade induced gene expression. Nucleoportin which redundantly inhibits flowering together with Nup98b through multiple pathways including clock, photoperiod, and age pathways. Gates flowering in a CONSTANS (CO)-independent mode and bypasses the CO checkpoint in photoperiodic signaling and integrated signals from multiple pathways to directly target FLOWERING LOCUS T (FT) for flowering control. |
| HanXRQr2_Chr14g0659991 | 1.459928 | 0.0232543 | ANGUSTIFOLIA 3 (AN3);GRF1-INTERACTING FACTOR (GIF);ARABIDOPSIS GRF1-INTERACTING FACTOR 1 (ATGIF1);GRF1-INTERACTING FACTOR 1 (GIF1) | Encodes a protein with similarity to mammalian transcriptional coactivator that is involved in cell proliferation during leaf and flower development. Loss of function mutations have narrow, pointed leaves and narrow floral organs. AN3 interacts with members of the growth regulating factor (GRF) family of transcription factors. |
| HanXRQr2_Chr10g0451751 | -4.006789 | 0.0263266 | NA | NA |
| HanXRQr2_Chr11g0509401 | -5.063111 | 0.0269591 | ACH1, ATNRT2.1, ATNRT2:1, LATERAL ROOT INITIATION 1, LIN1, NITRATE TRANSPORTER 2, NITRATE TRANSPORTER 2.1, NITRATE TRANSPORTER 2:1, NRT2, NRT2.1, NRT2:1, NRT2;1AT | High-affinity nitrate transporter. Up-regulated by nitrate. Functions as a repressor of lateral root initiation independently of nitrate uptake. |
| HanXRQr2_Chr11g0492561 | 1.125229 | 0.0272845 | OCTOPUS (OPS) | Encodes a polarly localised membrane-associated protein that regulates phloem differentiation entry. |
| HanXRQr2_Chr05g0227611 | 1.669631 | 0.0311078 | ATSWEET10, SWEET10 | Encodes a member of the SWEET sucrose efflux transporter family proteins. |
| HanXRQr2_Chr01g0024991 | -1.343977 | 0.0344978 | ACA1 | Encodes a chloroplast envelope Ca2+-ATPase with an N-terminal autoinhibitor. |
| HanXRQr2_Chr06g0271251 | 2.997483 | 0.0411330 | ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1);ENLARGED FIL EXPRESSION DOMAIN 1 (ENF1);SUCCINIC SEMIALDEHYDE DEHYDROGENASE (SSADH);SUCCINIC SEMIALDEHYDE DEHYDROGENASE 1 (SSADH1) | Encodes a mitochondrial succinic semialdehyde dehydrogenase (SSADH). Nomenclature according to Kirch, et al (2004). |
2 Overlaps
2.1 All Tissues
plyr::join_all(list(
overlap.root %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene,`gene name`,`gene description`),
overlap.shoot %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.node %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.leaf %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.meristem %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.earlyBudding %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.lateBudding %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.endosperm %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene),
overlap.seedcoat %>%
dplyr::filter(FDR < 0.05, abs(logFC) > 1, sweep_gene == "yes") %>%
dplyr::select(gene)
),
by="gene", type="inner") %>%
# format the table
knitr::kable(.) %>%
kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))| gene | gene name | gene description |
|---|---|---|
| HanXRQr2_Chr13g0578191 | OVA4, OVULE ABORTION 4 | Nucleotidylyl transferase superfamily protein |
| HanXRQr2_Chr11g0493381 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein;(source:Araport11) |
| HanXRQr2_Chr13g0578201 | 0 | Zinc finger C-x8-C-x5-C-x3-H type family protein;(source:Araport11) |
| HanXRQr2_Chr04g0160001 | (GCPE); (ISPG);CONSTITUTIVE SUBTILISIN 3 (CSB3);CHLOROPLAST BIOGENESIS 4 (CLB4);4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE (HDS) | Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP+ reductase. The mRNA is cell-to-cell mobile. |
| HanXRQr2_Chr07g0311551 | LHP1-INTERACTING FACTOR 2, LIF2 | Encodes a heterogeneous nuclear ribonucleoprotein (hnRNP-Q) that is involved in the plant innate immune response and may function as a suppressor of cell-autonomous immunity. |
| HanXRQr2_Chr05g0230361 | FTSH PROTEASE 11 (FTSH11) | encodes an FtsH protease that is localized to the chloroplast and the mitochondrion |
| HanXRQr2_Chr16g0749261 | ZINC TRANSPORTER 10 PRECURSOR (ZIP10) | member of Fe(II) transporter isolog family |
| HanXRQr2_Chr06g0261551 | PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK) | Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues. |
| HanXRQr2_Chr09g0380251 | CONSTITUTIVE EXPRESSER OF PR GENES 30 (CPR30);CONSTITUTIVE EXPRESSER OF PR GENES 1 (CPR1) | Encodes CPR1 (Constitutive Expresser of PR Genes 1, also known as CPR30), a F-Box protein that functions as a negative regulator of defense response and targets resistance proteins. |
3 sessionInfo
sessionInfo()## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] vroom_1.3.2 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2
## [5] purrr_0.3.4 readr_1.3.1 tidyr_1.1.2 tibble_3.0.3
## [9] ggplot2_3.3.2 tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.1.0 xfun_0.18 haven_2.3.1 colorspace_1.4-1
## [5] vctrs_0.3.4 generics_0.0.2 viridisLite_0.3.0 htmltools_0.5.0
## [9] yaml_2.2.1 blob_1.2.1 rlang_0.4.7 pillar_1.4.6
## [13] glue_1.4.2 withr_2.3.0 DBI_1.1.0 bit64_4.0.5
## [17] dbplyr_1.4.4 modelr_0.1.8 readxl_1.3.1 plyr_1.8.6
## [21] lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0
## [25] rvest_0.3.6 kableExtra_1.2.1 codetools_0.2-16 evaluate_0.14
## [29] knitr_1.30 fansi_0.4.1 highr_0.8 broom_0.7.0
## [33] Rcpp_1.0.5 scales_1.1.1 backports_1.1.10 webshot_0.5.2
## [37] jsonlite_1.7.1 bit_4.0.4 fs_1.5.0 hms_0.5.3
## [41] digest_0.6.25 stringi_1.5.3 grid_3.6.3 cli_2.0.2
## [45] tools_3.6.3 magrittr_1.5 crayon_1.3.4 pkgconfig_2.0.3
## [49] ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0 lubridate_1.7.9
## [53] assertthat_0.2.1 rmarkdown_2.3 httr_1.4.2 rstudioapi_0.11
## [57] R6_2.4.1 compiler_3.6.3